Alignments for a candidate for fadA in Hippea alviniae EP5-r

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Hippea alviniae EP5-r

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_022671372.1 G415_RS0109095 thiolase family protein

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000420385.1:WP_022671372.1
          Length = 389

 Score =  380 bits (976), Expect = e-110
 Identities = 186/391 (47%), Positives = 273/391 (69%), Gaps = 3/391 (0%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           M  V +   +R+  G +G +L  + A ++ +  +KE + + GI  EDV+ +I+GNVL AG
Sbjct: 1   MDGVFVVEPLRSPFGGFGGTLSSLSASEIASFVVKEILSRTGI--EDVDGLIMGNVLSAG 58

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
           +GQ+PARQ   K+GLP  + A+T+NKVCGSGL+++ LAAQ IK  D+ +IIAGGME+MS 
Sbjct: 59  VGQSPARQVIIKSGLPYSVNALTVNKVCGSGLKSLMLAAQSIKLKDSSLIIAGGMESMSN 118

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180
           APY  + AR+GYRMG+ + +D MI DGLWD +N+ HMG  AE +A+   I+R+ QD++A+
Sbjct: 119 APYYLSKARFGYRMGDGRAIDGMIFDGLWDVYNNVHMGYLAEMVAKAKKITRKIQDDYAV 178

Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGT 240
            S K+A+ + ++G FK+EIVP+ I  RKG  VVD DE P F    E + KLKPAF +DGT
Sbjct: 179 LSYKRAQHSAENGVFKEEIVPIEISSRKGVNVVDRDEEP-FRVDFEKIPKLKPAFVEDGT 237

Query: 241 VTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAI 300
           +TA NAS ++D AA  ++   +  K  G++P+AK+V+Y    +DP +    P  A +  +
Sbjct: 238 ITAANASTISDGAAAFIVADYDAIKRFGLEPIAKVVAYSEFSLDPKLFPLAPIGAIEKLL 297

Query: 301 EKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVT 360
           +K G  V+++DL E NEAF+   LA  ++LK D+++VNVNGGA++LGHP+GASGAR++V+
Sbjct: 298 KKTGLDVNDIDLFEINEAFSCVVLAALEELKLDIDRVNVNGGAVSLGHPLGASGARLVVS 357

Query: 361 LVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391
           L   M++R+AK G+A LCIGGG+  A L E+
Sbjct: 358 LTREMRRRNAKYGIAALCIGGGEAVATLFER 388


Lambda     K      H
   0.315    0.132    0.375 

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: 427
Number of extensions: 17
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: 392
Length of database: 389
Length adjustment: 31
Effective length of query: 361
Effective length of database: 358
Effective search space:   129238
Effective search space used:   129238
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_022671372.1 G415_RS0109095 (thiolase family protein)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.2920324.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-133  429.7   0.0   5.7e-133  429.5   0.0    1.0  1  NCBI__GCF_000420385.1:WP_022671372.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022671372.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.5   0.0  5.7e-133  5.7e-133       1     385 []       6     387 ..       6     387 .. 0.98

  Alignments for each domain:
  == domain 1  score: 429.5 bits;  conditional E-value: 5.7e-133
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           +v+ +R+p+g +gg+l++lsa+++++ v+ke+l r+g++  ++d +i+Gnvl+ag ++++aR++++++glp+s
  NCBI__GCF_000420385.1:WP_022671372.1   6 VVEPLRSPFGGFGGTLSSLSASEIASFVVKEILSRTGIE--DVDGLIMGNVLSAGVGQSPARQVIIKSGLPYS 76 
                                           68999*****99************************998..8******************************* PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           v+altvn+vC+Sgl++++laaq+ik  + ++++aGG+EsmS++p++l+++  r ++++g+ +  d ++ d+  
  NCBI__GCF_000420385.1:WP_022671372.1  77 VNALTVNKVCGSGLKSLMLAAQSIKLKDSSLIIAGGMESMSNAPYYLSKA--RFGYRMGDGRAIDGMIFDGlw 147
                                           ************************************************98..89**************999** PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            v+++++mg  Ae++ak ++i+R+ qD+ya+ S+++a+++ e+g fk+eivp+e+  +   +vv++De++  +
  NCBI__GCF_000420385.1:WP_022671372.1 148 dVYNNVHMGYLAEMVAKAKKITRKIQDDYAVLSYKRAQHSAENGVFKEEIVPIEISSRkgVNVVDRDEEPF-R 219
                                           *99****************************************************9999999999999987.8 PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                           +  ek+ kLkpaf e +g t+tA+N+s ++DGAaa++++  ++ k++gl+p+a++v++++ ++dp+ ++l+p+
  NCBI__GCF_000420385.1:WP_022671372.1 220 VDFEKIPKLKPAFVE-DG-TITAANASTISDGAAAFIVADYDAIKRFGLEPIAKVVAYSEFSLDPKLFPLAPI 290
                                           *************96.9*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                            Aiek+Lkk+gl+++didl+EinEAF+ +vla+ +el+ ld ++vNvnGGA++lGHPlGasGar+v++l +e+
  NCBI__GCF_000420385.1:WP_022671372.1 291 GAIEKLLKKTGLDVNDIDLFEINEAFSCVVLAALEELK-LDIDRVNVNGGAVSLGHPLGASGARLVVSLTREM 362
                                           **************************************.89******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           ++r++kyG+a+lC+ggG ++A+++e
  NCBI__GCF_000420385.1:WP_022671372.1 363 RRRNAKYGIAALCIGGGEAVATLFE 387
                                           **********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (389 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.98
//
[ok]

This GapMind analysis is from Apr 09 2024. 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