Alignments for a candidate for acs in Luteimonas huabeiensis HB2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Luteimonas huabeiensis HB2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_043688887.1 Z164_RS19710 acetate--CoA ligase

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



>NCBI__GCF_000559025.1:WP_043688887.1
          Length = 650

 Score =  883 bits (2282), Expect = 0.0
 Identities = 418/646 (64%), Positives = 503/646 (77%), Gaps = 1/646 (0%)

Query: 2   SAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFD 61
           S   +YPV   +AA T      Y  +Y++SV +PD FW   A RLDW+ P T ++  SF 
Sbjct: 3   STPDVYPVPESIAADTAIGPEDYARLYEESVRDPDAFWGRAAGRLDWMTPPTRIRDVSFR 62

Query: 62  DHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPS-ESRNITYRELHEEVCKF 120
                I+W+ DG LN S NCLDRHLA RGD+ A+IWE DDPS E+R++TYRELH  VC+ 
Sbjct: 63  QEDFRIRWYDDGELNASVNCLDRHLASRGDKTALIWEPDDPSNEARHVTYRELHARVCRL 122

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANA+R   V +GD VTIY+PMI EA V MLAC RIGA+HSVVFGGFSP ++A R+ DC S
Sbjct: 123 ANAMRSLGVGKGDRVTIYLPMIVEAAVTMLACARIGAVHSVVFGGFSPGSIADRVADCGS 182

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           K+++TADEG+R G++IPLKANVD AL  P T +++ V+V + T G ++    RD WY+ +
Sbjct: 183 KLIVTADEGLRGGRRIPLKANVDAALKMPGTQTVETVLVVRHTGGAVEMQMPRDRWYDAV 242

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           +      C P+ M AE+ LFILYTSGSTGKPKGV HTT GYL+YA+ THE VFD K  ++
Sbjct: 243 VDDQPETCEPERMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASYTHEAVFDLKEDDI 302

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGWVTGHSYIVYGPLANGAT+L+FEGVPNYP+++R   V+DKH+V+I YTAPTA
Sbjct: 303 YWCTADVGWVTGHSYIVYGPLANGATSLVFEGVPNYPNVSRFWDVVDKHRVTIFYTAPTA 362

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+M  G A V+ A  +SLR+LG+VGEPINPEAW WY++ VG  RCP+VDTWWQTETGG
Sbjct: 363 IRALMREGEAPVKAASRASLRILGTVGEPINPEAWRWYFEVVGDGRCPVVDTWWQTETGG 422

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LI+PLPGA   KPGSAT+PFFG+ PA+VD  G +++G AEGNLVILDSWPGQ RT+YGD
Sbjct: 423 ILIAPLPGAIPAKPGSATKPFFGIRPAIVDAQGTVLDGEAEGNLVILDSWPGQMRTVYGD 482

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H RF+DTYF  + G YFTGDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+HP
Sbjct: 483 HQRFIDTYFSAYPGTYFTGDGCRRDADGYYWITGRVDDVINVSGHRIGTAEVESALVSHP 542

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVG PHDIKGQGIY YVTL AGE+ S+ L  EL   VRKEIGPIASPD +QWAP
Sbjct: 543 KVAEAAVVGFPHDIKGQGIYAYVTLVAGEQGSDELLKELVAHVRKEIGPIASPDHLQWAP 602

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHK 646
           GLPKTRSGKIMRRILRKIA    D LGD +TLADP VV  L++  +
Sbjct: 603 GLPKTRSGKIMRRILRKIAENAPDQLGDTTTLADPSVVDALVKQRR 648


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: 1421
Number of extensions: 63
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: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
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_043688887.1 Z164_RS19710 (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.3471898.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1020.4   0.0          0 1020.2   0.0    1.0  1  NCBI__GCF_000559025.1:WP_043688887.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000559025.1:WP_043688887.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1020.2   0.0         0         0       4     628 ..      22     645 ..      19     646 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1020.2 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                            e+y++lyee+++dp++fw++ a  +l+w++p ++++d s+++   +++W++dgeln+s+nc+drh+++r dk
  NCBI__GCF_000559025.1:WP_043688887.1  22 PEDYARLYEESVRDPDAFWGRAAG-RLDWMTPPTRIRDVSFRQedfRIRWYDDGELNASVNCLDRHLASRGDK 93 
                                           589*****************9999.5*************99887789************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +a+iwe d++++++r++tY+el+++vcrlan++++lGv kgdrv+iYlpmi+ea+++mlacaRiGavhsvvf+
  NCBI__GCF_000559025.1:WP_043688887.1  94 TALIWEPDDPSNEARHVTYRELHARVCRLANAMRSLGVGKGDRVTIYLPMIVEAAVTMLACARIGAVHSVVFG 166
                                           ************************************************************************* PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfs+ ++a+R+ d+ +kl++tadeglRgg++i+lk++vd+al++  + +ve+vlvv++tg  v+ ++  rD w
  NCBI__GCF_000559025.1:WP_043688887.1 167 GFSPGSIADRVADCGSKLIVTADEGLRGGRRIPLKANVDAALKMPGTqTVETVLVVRHTGGAVE-MQMPRDRW 238
                                           ********************************************9888**************66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           ++ +v++ ++++cepe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t++ vfd+k++di+wCtaDvG
  NCBI__GCF_000559025.1:WP_043688887.1 239 YDAVVDD-QPETCEPERMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASYTHEAVFDLKEDDIYWCTADVG 310
                                           ******7.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           WvtGhsYivygPLanGat+l+fegvp+yp+ srfw+v++k++vtifYtaPtaiRalm++ge+ vk+ ++ slr
  NCBI__GCF_000559025.1:WP_043688887.1 311 WVTGHSYIVYGPLANGATSLVFEGVPNYPNVSRFWDVVDKHRVTIFYTAPTAIRALMREGEAPVKAASRASLR 383
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lg+vGepinpeaw+Wy+evvG+++cp+vdtwWqtetGgili+plpg a+++kpgsat+P+fGi++++vd +g
  NCBI__GCF_000559025.1:WP_043688887.1 384 ILGTVGEPINPEAWRWYFEVVGDGRCPVVDTWWQTETGGILIAPLPG-AIPAKPGSATKPFFGIRPAIVDAQG 455
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                           + ++ e+e g Lvi ++wP+++rt+ygd++rf++tYf++++g+yftGDg+rrd+dGy+wi+GRvDdvinvsGh
  NCBI__GCF_000559025.1:WP_043688887.1 456 TVLDGEAE-GNLVILDSWPGQMRTVYGDHQRFIDTYFSAYPGTYFTGDGCRRDADGYYWITGRVDDVINVSGH 527
                                           ***98887.79************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           r+gtae+esalvsh++vaeaavvg+p++ikg+ i+a+v+l +g++ ++e l kel ++vrkeigpia+pd+++
  NCBI__GCF_000559025.1:WP_043688887.1 528 RIGTAEVESALVSHPKVAEAAVVGFPHDIKGQGIYAYVTLVAGEQGSDE-LLKELVAHVRKEIGPIASPDHLQ 599
                                           *********************************************9995.*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkiae++ ++lgd++tl+dpsvv++l +
  NCBI__GCF_000559025.1:WP_043688887.1 600 WAPGLPKTRSGKIMRRILRKIAENApDQLGDTTTLADPSVVDALVK 645
                                           ******************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (650 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 29.19
//
[ok]

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

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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 2024 update 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