Alignments for a candidate for acs in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Stenotrophomonas chelatiphaga DSM 21508

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_057507083.1 ABB28_RS02385 acetate--CoA ligase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>NCBI__GCF_001431535.1:WP_057507083.1
          Length = 647

 Score =  879 bits (2271), Expect = 0.0
 Identities = 423/644 (65%), Positives = 499/644 (77%), Gaps = 1/644 (0%)

Query: 4   ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63
           A LYPV P+ A +   D+ TY+  YQ S+  PD FW E A+RL W K  + +K  S+D  
Sbjct: 2   ADLYPVDPQFAKNARIDKTTYQQQYQASIDAPDAFWGEAAQRLQWFKQPSIIKNVSYDLA 61

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDP-SESRNITYRELHEEVCKFAN 122
              IKWF DG LN S NCLDR L +RG++ A+++E D P + ++++TYREL+E  C+  N
Sbjct: 62  DFRIKWFEDGELNASVNCLDRQLEKRGEKTALLFEPDSPDAPAQHVTYRELYERTCRLGN 121

Query: 123 ALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKV 182
           ALR   V +GD VTIY+PMI +A VAMLAC RIGAIHSVVFGGF+P ++A R+ DC SK+
Sbjct: 122 ALRNLGVKKGDRVTIYLPMIVDAAVAMLACARIGAIHSVVFGGFAPNSIADRVSDCASKL 181

Query: 183 VITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMK 242
           +ITADEG+R GKKIPLKANVD AL  P T++++ V+V + T G +     RD W+ D++ 
Sbjct: 182 IITADEGLRGGKKIPLKANVDAALKLPGTNTVETVLVVRHTGGAVDMQAPRDRWFHDVVD 241

Query: 243 VAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYW 302
                C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLLYAA THE VFD +  ++YW
Sbjct: 242 SQPAECEPERMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAYTHEAVFDLREDDIYW 301

Query: 303 CTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIR 362
           CTADVGWVTGHSYIVYGPLANGAT+L+FEGVPNYPD +R   VIDKHKVS+ YTAPTAIR
Sbjct: 302 CTADVGWVTGHSYIVYGPLANGATSLMFEGVPNYPDTSRFWNVIDKHKVSLFYTAPTAIR 361

Query: 363 AMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVL 422
           A+M  G   V+    +SLRLLGSVGEPINPEAW WYY+ VG  RCPIVDTWWQTETGG+L
Sbjct: 362 ALMREGEEPVKRTSRASLRLLGSVGEPINPEAWRWYYEVVGDSRCPIVDTWWQTETGGIL 421

Query: 423 ISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHD 482
           ISPLPGA  LKPGSA+ PFFGV PALV+  G + +GA EGNL+I DSWPGQ RT+YGD  
Sbjct: 422 ISPLPGAVDLKPGSASLPFFGVQPALVNADGEIKDGATEGNLIIRDSWPGQMRTVYGDDQ 481

Query: 483 RFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKV 542
           RF+DTYF+T+ G YFTGDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+HPKV
Sbjct: 482 RFIDTYFRTYPGAYFTGDGCRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKV 541

Query: 543 AEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGL 602
           AEAAVVG PH++KGQGIY YVTL A E  SE L  EL  WVRKEIGPIA+PD +QWAPGL
Sbjct: 542 AEAAVVGFPHEVKGQGIYAYVTLIADEAPSEELHKELVAWVRKEIGPIATPDHLQWAPGL 601

Query: 603 PKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHK 646
           PKTRSGKIMRRILRKIA    D LGD STLADP VVA L++  K
Sbjct: 602 PKTRSGKIMRRILRKIAENAPDQLGDTSTLADPSVVASLVDERK 645


Lambda     K      H
   0.318    0.135    0.418 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1394
Number of extensions: 53
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 647
Length adjustment: 38
Effective length of query: 613
Effective length of database: 609
Effective search space:   373317
Effective search space used:   373317
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_057507083.1 ABB28_RS02385 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.2520.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-307 1005.7   0.0   4.4e-307 1005.4   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057507083.1  ABB28_RS02385 acetate--CoA ligas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507083.1  ABB28_RS02385 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1005.4   0.0  4.4e-307  4.4e-307       4     627 ..      19     641 ..      16     643 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1005.4 bits;  conditional E-value: 4.4e-307
                                 TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvek 69 
                                                ++y++ y+ +i+ p++fw++ a+ +l+w+k+ + +++ s +    ++kWfedgeln+s+nc+dr++ek
  lcl|NCBI__GCF_001431535.1:WP_057507083.1  19 KTTYQQQYQASIDAPDAFWGEAAQ-RLQWFKQPSIIKNVSYDLadfRIKWFEDGELNASVNCLDRQLEK 86 
                                               678*****************9999.5******999998887655579********************** PP

                                 TIGR02188  70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
                                               r +k+a+ +e d+++  ++++tY+el++++crl n+l++lGvkkgdrv+iYlpmi++a++amlacaRiG
  lcl|NCBI__GCF_001431535.1:WP_057507083.1  87 RGEKTALLFEPDSPDAPAQHVTYRELYERTCRLGNALRNLGVKKGDRVTIYLPMIVDAAVAMLACARIG 155
                                               ***************9***************************************************** PP

                                 TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtge 206
                                               a+hsvvf+Gf+++++a+R+ d+ +kl+itadeglRggk+i+lk++vd+al+   + +ve+vlvv++tg 
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 156 AIHSVVFGGFAPNSIADRVSDCASKLIITADEGLRGGKKIPLKANVDAALKLPGTnTVETVLVVRHTGG 224
                                               ***************************************************99888************* PP

                                 TIGR02188 207 evaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyv 275
                                                v  ++  rD w++++v++ ++aecepe++++edplfiLYtsGstGkPkGvlhttgGyll+aa+t++ v
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 225 AVD-MQAPRDRWFHDVVDS-QPAECEPERMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAYTHEAV 291
                                               *66.**************5.************************************************* PP

                                 TIGR02188 276 fdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtai 344
                                               fd++++di+wCtaDvGWvtGhsYivygPLanGat+l+fegvp+ypd+srfw+vi+k+kv+ fYtaPtai
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 292 FDLREDDIYWCTADVGWVTGHSYIVYGPLANGATSLMFEGVPNYPDTSRFWNVIDKHKVSLFYTAPTAI 360
                                               ********************************************************************* PP

                                 TIGR02188 345 RalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgva 413
                                               Ralm++gee vk++++ slr+lgsvGepinpeaw+WyyevvG+++cpivdtwWqtetGgili+plpg a
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 361 RALMREGEEPVKRTSRASLRLLGSVGEPINPEAWRWYYEVVGDSRCPIVDTWWQTETGGILISPLPG-A 428
                                               *******************************************************************.6 PP

                                 TIGR02188 414 telkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyf 482
                                               ++lkpgsa+lP+fG+++++v+ +g+  +  +e g L+i+++wP+++rt+ygd++rf++tYf++++g yf
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 429 VDLKPGSASLPFFGVQPALVNADGEIKDGATE-GNLIIRDSWPGQMRTVYGDDQRFIDTYFRTYPGAYF 496
                                               ************************98886666.89********************************** PP

                                 TIGR02188 483 tGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
                                               tGDg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalvsh++vaeaavvg+p+e+kg+ i+a+v+l 
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 497 TGDGCRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVAEAAVVGFPHEVKGQGIYAYVTLI 565
                                               ********************************************************************* PP

                                 TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstled 619
                                               + ++++ee l+kel ++vrkeigpia+pd++++++ lPktRsGkimRR+lrkiae++ ++lgd+stl+d
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 566 ADEAPSEE-LHKELVAWVRKEIGPIATPDHLQWAPGLPKTRSGKIMRRILRKIAENApDQLGDTSTLAD 633
                                               *****995.************************************************************ PP

                                 TIGR02188 620 psvveelk 627
                                               psvv++l 
  lcl|NCBI__GCF_001431535.1:WP_057507083.1 634 PSVVASLV 641
                                               ****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (647 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.04
# Mc/sec: 8.92
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources