Alignments for a candidate for acs in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Jannaschia aquimarina GSW-M26

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_043920483.1 jaqu_RS18400 acetate--CoA ligase

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>NCBI__GCF_000877395.1:WP_043920483.1
          Length = 655

 Score =  847 bits (2188), Expect = 0.0
 Identities = 414/644 (64%), Positives = 488/644 (75%), Gaps = 9/644 (1%)

Query: 7   YPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           +P   E+AA+   D ATY AMYQ S+ +P+ FW E  KRLDWIKP+  VK T+F    V 
Sbjct: 9   FPPSDEMAASAHADRATYDAMYQASIEDPEAFWGEHGKRLDWIKPYGRVKDTTFGPGEVS 68

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAE-----SRNITYRELHEQVCKFA 121
           IKWF DGTLNVS NC+DRHLAERGDQ AIIWE DDP       +++ITYR+LH  VCK A
Sbjct: 69  IKWFEDGTLNVSSNCIDRHLAERGDQTAIIWEPDDPNSVDGGGAQHITYRQLHSHVCKMA 128

Query: 122 NALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSK 181
           N L+   V RGD V +Y+PMIP+A  AMLAC RIGAIHS+VF GFS +AL  RI  C +K
Sbjct: 129 NVLKALGVSRGDRVVLYLPMIPQAAYAMLACARIGAIHSIVFAGFSADALGARIDACDAK 188

Query: 182 VVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLM 241
           VVIT+D   R G++ +LK NV+ AL N       K +V KRTG  I W    D W  +  
Sbjct: 189 VVITSDGAPRGGRQTNLKDNVNQALLNDFDEV--KCLVVKRTGQQIAWRNGLDYWLHEEE 246

Query: 242 KVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIY 301
           +     C  +EMGAE+ LFILYTSGSTG+PKGV HT+GGYL+YAA+TH+ VFDY+ G+I+
Sbjct: 247 EKVSDDCPAEEMGAEDPLFILYTSGSTGQPKGVVHTSGGYLVYAAMTHQYVFDYKDGDIF 306

Query: 302 WCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAI 361
           WCTADVGWVTGH+YIVYGPLANGATT++FEGVP +PD  R  ++  KHKVN  YTAPTAI
Sbjct: 307 WCTADVGWVTGHSYIVYGPLANGATTVMFEGVPTFPDAGRFWEVCAKHKVNQFYTAPTAI 366

Query: 362 RAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGAT 421
           RA+M +G   V   D SSLR+LG+VGEPINPEAW WY + VGQSRCPIVDTWWQTETG  
Sbjct: 367 RALMGKGDEFVSKHDLSSLRILGTVGEPINPEAWNWYNEVVGQSRCPIVDTWWQTETGGH 426

Query: 422 LMSPLPGAHGLKPGSAARPFFGVVPALVD-NLGNIIEGV-AEGNLVILDSWPGQARTLYG 479
           L++PLPGA  LKPGSA  PFFGV P +++   G +I+   AEG L + DSWPGQ RT++G
Sbjct: 427 LLTPLPGATPLKPGSATLPFFGVQPVVLEPQTGEVIQDTEAEGVLCMADSWPGQMRTVWG 486

Query: 480 DHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAH 539
           DH+RFV TYF  ++G YFTGDG RRDADGY+WITGRVDDV+NVSGHRMGTAE+ESA+VAH
Sbjct: 487 DHERFVKTYFSDYKGYYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAH 546

Query: 540 PKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWA 599
            KVAEAAVVG PH +KGQGIY YVTL GG +P++ LR EL +WVRKEIGPIA PD IQWA
Sbjct: 547 SKVAEAAVVGYPHPVKGQGIYAYVTLMGGVDPTDELRKELSDWVRKEIGPIAKPDCIQWA 606

Query: 600 PGLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLID 643
           PGLPKTRSGKIMRRILRKIA  +Y  LGD STLA+P VV  LI+
Sbjct: 607 PGLPKTRSGKIMRRILRKIAENDYGSLGDTSTLAEPEVVDDLIE 650


Lambda     K      H
   0.319    0.136    0.425 

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: 1509
Number of extensions: 76
Number of successful extensions: 4
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: 655
Length adjustment: 38
Effective length of query: 613
Effective length of database: 617
Effective search space:   378221
Effective search space used:   378221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_043920483.1 jaqu_RS18400 (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.1911921.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 1015.9   0.0          0 1015.7   0.0    1.0  1  NCBI__GCF_000877395.1:WP_043920483.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000877395.1:WP_043920483.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1015.7   0.0         0         0       4     628 ..      23     650 ..      20     651 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1015.7 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                             +y ++y+ +iedpe+fw++++k +l+w+kp+ +v+d+++ p   ++kWfedg+lnvs nc+drh+++r d+
  NCBI__GCF_000877395.1:WP_043920483.1  23 RATYDAMYQASIEDPEAFWGEHGK-RLDWIKPYGRVKDTTFGPgevSIKWFEDGTLNVSSNCIDRHLAERGDQ 94 
                                           678*********************.5**************9988889************************** PP

                             TIGR02188  74 vaiiwegdeege....dsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhs 142
                                           +aiiwe d++++     ++++tY++l+++vc++anvlk+lGv +gdrv++Ylpmip+a++amlacaRiGa+hs
  NCBI__GCF_000877395.1:WP_043920483.1  95 TAIIWEPDDPNSvdggGAQHITYRQLHSHVCKMANVLKALGVSRGDRVVLYLPMIPQAAYAMLACARIGAIHS 167
                                           ********88876566789****************************************************** PP

                             TIGR02188 143 vvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegr 215
                                           +vfaGfsa+al  Ri  ++ak+vit+d++ Rgg++++lk++v++al +  ++v+ +lvvkrtg+++a w++g 
  NCBI__GCF_000877395.1:WP_043920483.1 168 IVFAGFSADALGARIDACDAKVVITSDGAPRGGRQTNLKDNVNQALLNDFDEVK-CLVVKRTGQQIA-WRNGL 238
                                           **********************************************99988887.9*********77.***** PP

                             TIGR02188 216 DvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCta 288
                                           D+w++e+ ek +s++c++e++++edplfiLYtsGstG+PkGv+ht+gGyl++aa+t++yvfd+kd+difwCta
  NCBI__GCF_000877395.1:WP_043920483.1 239 DYWLHEEEEK-VSDDCPAEEMGAEDPLFILYTSGSTGQPKGVVHTSGGYLVYAAMTHQYVFDYKDGDIFWCTA 310
                                           *********6.************************************************************** PP

                             TIGR02188 289 DvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdls 361
                                           DvGWvtGhsYivygPLanGatt++fegvpt+pda+rfwev+ k+kv++fYtaPtaiRalm +g+e+v+khdls
  NCBI__GCF_000877395.1:WP_043920483.1 311 DVGWVTGHSYIVYGPLANGATTVMFEGVPTFPDAGRFWEVCAKHKVNQFYTAPTAIRALMGKGDEFVSKHDLS 383
                                           ************************************************************************* PP

                             TIGR02188 362 slrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd 434
                                           slr+lg+vGepinpeaw+Wy+evvG+++cpivdtwWqtetGg+l+tplpg at+lkpgsatlP+fG++++v++
  NCBI__GCF_000877395.1:WP_043920483.1 384 SLRILGTVGEPINPEAWNWYNEVVGQSRCPIVDTWWQTETGGHLLTPLPG-ATPLKPGSATLPFFGVQPVVLE 455
                                           **************************************************.6********************* PP

                             TIGR02188 435 .eegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvin 506
                                            ++g+ ++++e +gvL++ ++wP+++rt++gd+erfv+tYf+++kg+yftGDg+rrd+dGy+wi+GRvDdvin
  NCBI__GCF_000877395.1:WP_043920483.1 456 pQTGEVIQDTEAEGVLCMADSWPGQMRTVWGDHERFVKTYFSDYKGYYFTGDGCRRDADGYYWITGRVDDVIN 528
                                           9999999999999************************************************************ PP

                             TIGR02188 507 vsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakp 579
                                           vsGhr+gtae+esalv+h++vaeaavvg+p+ +kg+ i+a+v+l+ gv++++e l+kel ++vrkeigpiakp
  NCBI__GCF_000877395.1:WP_043920483.1 529 VSGHRMGTAEVESALVAHSKVAEAAVVGYPHPVKGQGIYAYVTLMGGVDPTDE-LRKELSDWVRKEIGPIAKP 600
                                           ****************************************************5.******************* PP

                             TIGR02188 580 dkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           d i++++ lPktRsGkimRR+lrkiae++  +lgd+stl++p+vv++l+e
  NCBI__GCF_000877395.1:WP_043920483.1 601 DCIQWAPGLPKTRSGKIMRRILRKIAENDyGSLGDTSTLAEPEVVDDLIE 650
                                           *****************************99***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (655 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: 00:00:00.02
# Mc/sec: 17.41
//
[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