GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas litoralis 2SM5

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_090271795.1 BLU11_RS01910 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_900105005.1:WP_090271795.1
          Length = 647

 Score =  826 bits (2133), Expect = 0.0
 Identities = 392/647 (60%), Positives = 496/647 (76%), Gaps = 7/647 (1%)

Query: 1   MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTS 59
           M +I  H +  N   +  ++   YE MY+QSI  PD FW EQ  + ++W++P+ KV  ++
Sbjct: 1   MYKIQNHKVSENQLRQTHLDQDGYERMYRQSIEQPDMFWAEQANRFVEWMQPWSKVHESN 60

Query: 60  FAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119
              G  +  W+ D  LN++ NC+DRHL+   D+TAIIWEGDD + S++I+Y+ELH +VCR
Sbjct: 61  MEKGEAA--WFVDAKLNVSVNCIDRHLKTRADQTAIIWEGDDPNDSRYITYRELHEEVCR 118

Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179
            AN L E G+KKGD V +YMPM+PEAA AMLACARIGAVH+V+FGGFSPEA+  RI ++ 
Sbjct: 119 LANVLKERGVKKGDRVCLYMPMIPEAAFAMLACARIGAVHTVVFGGFSPEALRDRIQNAE 178

Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKN-PNVTSVEHVVVLKRTGGKIDWQEGRDLWWH 238
             +VIT+DEGVR G+++PLK+NVD AL   PNV +V   V +KRTG  + W E +D+W+H
Sbjct: 179 CDVVITADEGVRGGKTVPLKQNVDKALTACPNVHTV---VTVKRTGADVAWDEQKDVWYH 235

Query: 239 DLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPG 298
           +   Q S +   E M++EDPLFILYTSGSTGKPKGVLHTTGGYLV  ALT  YVFDYH G
Sbjct: 236 EACAQVSKECTPEPMDSEDPLFILYTSGSTGKPKGVLHTTGGYLVSVALTHHYVFDYHDG 295

Query: 299 DIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAP 358
           +++WCTADVGWVTGHSY++YGPL  GATTLMFEGVP +PT +R  +VVDKH+VN+ YTAP
Sbjct: 296 EVFWCTADVGWVTGHSYIVYGPLCNGATTLMFEGVPTYPTASRCWEVVDKHKVNVFYTAP 355

Query: 359 TAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTET 418
           TAIRALMA G++ ++ + R S+R+LGSVGEPINPE WEWY++ +G+ +CP+VDTWWQTET
Sbjct: 356 TAIRALMALGEEPVKSSSRESIRLLGSVGEPINPEVWEWYYQVVGDSRCPIVDTWWQTET 415

Query: 419 GGFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLF 478
           G  +I PLPGA  LK G+A RP FGV PALVDNEGN L+G  +G+LVI  SWP Q RT++
Sbjct: 416 GSILIAPLPGACGLKPGAAMRPMFGVVPALVDNEGNELDGVADGNLVIKQSWPSQIRTVY 475

Query: 479 GDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVA 538
           GDH R  +TYFST+K +YF+GDGARRD DG YWITGRVDDVLN+SGHR+GTAE+ESALV 
Sbjct: 476 GDHHRLIETYFSTYKGVYFTGDGARRDADGDYWITGRVDDVLNISGHRIGTAEVESALVL 535

Query: 539 HPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHW 598
           +  +AEAAVVG PH+IKGQAIYAYV    G   + E+ AE++  V +++G  A PD +  
Sbjct: 536 NDYVAEAAVVGCPHDIKGQAIYAYVMPMKGVTLTDEVMAELKVAVSEQVGAFARPDFIQP 595

Query: 599 TDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           T  LPKTRSGKIMRRILRKIA  +   LGDTSTLADPGVV++L+E +
Sbjct: 596 TTGLPKTRSGKIMRRILRKIACDELDTLGDTSTLADPGVVDELVEHR 642


Lambda     K      H
   0.317    0.135    0.421 

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: 1360
Number of extensions: 52
Number of successful extensions: 3
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: 652
Length of database: 647
Length adjustment: 38
Effective length of query: 614
Effective length of database: 609
Effective search space:   373926
Effective search space used:   373926
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_090271795.1 BLU11_RS01910 (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.100747.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 1019.0   0.2          0 1018.8   0.2    1.0  1  NCBI__GCF_900105005.1:WP_090271795.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090271795.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.8   0.2         0         0       4     628 ..      21     640 ..      18     641 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1018.8 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                           ++ y+++y+++ie+p+ fwa++a++ +ew++p++kv ++++e+ +++Wf+d++lnvs+nc+drh+++r+d++a
  NCBI__GCF_900105005.1:WP_090271795.1  21 QDGYERMYRQSIEQPDMFWAEQANRFVEWMQPWSKVHESNMEKgEAAWFVDAKLNVSVNCIDRHLKTRADQTA 93 
                                           678*************************************9999***************************** PP

                             TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148
                                           iiwegd+++ dsr +tY+el++evcrlanvlke Gvkkgdrv++Y+pmipea++amlacaRiGavh+vvf+Gf
  NCBI__GCF_900105005.1:WP_090271795.1  94 IIWEGDDPN-DSRYITYRELHEEVCRLANVLKERGVKKGDRVCLYMPMIPEAAFAMLACARIGAVHTVVFGGF 165
                                           ********9.5************************************************************** PP

                             TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                           s+eal++Ri++ae+ +vitadeg+Rggk+++lk++vd+al++++ +v++v+ vkrtg++va w+e++Dvw++e
  NCBI__GCF_900105005.1:WP_090271795.1 166 SPEALRDRIQNAECDVVITADEGVRGGKTVPLKQNVDKALTACP-NVHTVVTVKRTGADVA-WDEQKDVWYHE 236
                                           *******************************************9.6*************77.*********** PP

                             TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294
                                           ++++ +s+ec+pe++dsedplfiLYtsGstGkPkGvlhttgGyl+ +alt++yvfd++d+++fwCtaDvGWvt
  NCBI__GCF_900105005.1:WP_090271795.1 237 ACAQ-VSKECTPEPMDSEDPLFILYTSGSTGKPKGVLHTTGGYLVSVALTHHYVFDYHDGEVFWCTADVGWVT 308
                                           ***6.******************************************************************** PP

                             TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367
                                           GhsYivygPL+nGattl+fegvptyp+asr+wev++k+kv++fYtaPtaiRalm+lgee vk+ +++s+r+lg
  NCBI__GCF_900105005.1:WP_090271795.1 309 GHSYIVYGPLCNGATTLMFEGVPTYPTASRCWEVVDKHKVNVFYTAPTAIRALMALGEEPVKSSSRESIRLLG 381
                                           ************************************************************************* PP

                             TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440
                                           svGepinpe weWyy+vvG+++cpivdtwWqtetG+ili+plpg a  lkpg+a++P+fG+ +++vd+eg+e+
  NCBI__GCF_900105005.1:WP_090271795.1 382 SVGEPINPEVWEWYYQVVGDSRCPIVDTWWQTETGSILIAPLPG-ACGLKPGAAMRPMFGVVPALVDNEGNEL 453
                                           ********************************************.6*************************** PP

                             TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513
                                           +  ++ g Lvik++wPs++rt+ygd++r++etYf+++kg+yftGDgarrd+dG++wi+GRvDdv+n+sGhr+g
  NCBI__GCF_900105005.1:WP_090271795.1 454 DGVAD-GNLVIKQSWPSQIRTVYGDHHRLIETYFSTYKGVYFTGDGARRDADGDYWITGRVDDVLNISGHRIG 525
                                           *8777.89***************************************************************** PP

                             TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586
                                           tae+esalv ++ vaeaavvg p++ikg+ai+a+v+ ++gv+ ++e + +elk +v++++g++a+pd i+ ++
  NCBI__GCF_900105005.1:WP_090271795.1 526 TAEVESALVLNDYVAEAAVVGCPHDIKGQAIYAYVMPMKGVTLTDE-VMAELKVAVSEQVGAFARPDFIQPTT 597
                                           *******************************************995.************************** PP

                             TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                            lPktRsGkimRR+lrkia +e ++lgd+stl+dp vv+el e
  NCBI__GCF_900105005.1:WP_090271795.1 598 GLPKTRSGKIMRRILRKIACDElDTLGDTSTLADPGVVDELVE 640
                                           ***************************************9976 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 34.95
//
[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:

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:

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:

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:

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