Alignments for a candidate for fahA in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Herbaspirillum autotrophicum IAM 14942

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_050464693.1 AKL27_RS20355 fumarylacetoacetase

Query= BRENDA::Q94272
         (418 letters)



>NCBI__GCF_001189915.1:WP_050464693.1
          Length = 447

 Score =  386 bits (991), Expect = e-112
 Identities = 219/435 (50%), Positives = 278/435 (63%), Gaps = 23/435 (5%)

Query: 1   MKSFVSVPQNSD--FPIQNLPYGVFSTKADSSR-HIGVAIGDQILNL--AEIANLF---D 52
           ++S+VS     D  FPIQNLPYG+F  +  S +   GVAIGDQIL+L  A  A  F   D
Sbjct: 13  LRSWVSSANADDNEFPIQNLPYGIFRRRGSSEQFRAGVAIGDQILDLRVAHAAGAFVAAD 72

Query: 53  GPQLKAHQDVFKQSTLNAFMALPRPAWLEARARIQQLLSEDCAVLRDNAHLRSRALVAQS 112
                A       +TLN  M L   AW   R  + +LL  DC+  +    L +  LVAQS
Sbjct: 73  AQTQAAVHAAVAGATLNPLMDLDAGAWSALRLALSRLLRSDCSAAQQA--LLTPCLVAQS 130

Query: 113 DATMHLPAQIGDYTDFYSSIHHATNVGIMFRGKENALMPNWKWLPVGYHGRASSIVVSGT 172
           DA   LPAQIGDYTDFY+SIHHAT +G +FR  +N L+PN+KW+P+GYHGRASSI VSG 
Sbjct: 131 DAEHALPAQIGDYTDFYTSIHHATAIGKLFR-PDNPLLPNYKWVPIGYHGRASSIDVSGQ 189

Query: 173 DLKRPVGQTKAPDAEVPSFGPSKLMDFELEMAFFVGGPENELGTRVPIEKAEDRIFGVVL 232
             +RP+GQT+APDAEVP FGP K +D+ELE+  F+G   N LG  +P+  AE  +FG+ L
Sbjct: 190 QFRRPLGQTRAPDAEVPVFGPCKRLDYELEVGVFIGNG-NALGEAIPMANAEAHVFGLCL 248

Query: 233 MNDWSARDIQAWEYVPLGPFLAKSFATTVSPWVVSIEALRPYFV--ENPVQDPVPPAYLH 290
           +NDWSARD+QAWEY PLGPFLAK+FA+T+SPW+V++EAL PY         DP P  YL 
Sbjct: 249 LNDWSARDMQAWEYQPLGPFLAKNFASTISPWIVTLEALAPYRAGWTRDSADPQPLPYLD 308

Query: 291 H---DDPFTLDINLAVSIRP----EGDAVDHIVCKTNFKHLYWTLKQQLAHHTVNGCNLR 343
                D   LD+ L V I+           H +  +NF+  YW++ Q +AHHTVNGCNLR
Sbjct: 309 DAGLRDHGALDVQLEVLIQTPAMRSAGLAPHRLSLSNFRDSYWSVSQLVAHHTVNGCNLR 368

Query: 344 AGDLLGSGTVSGPEEGAYGSMLELSWRGAKEVPV-GSEIRKFLKDGDEVNLSGVCEKNG- 401
            GDLLGSGT SGP   A GS+LEL+  G + + + G E R F++DGD + + G   ++G 
Sbjct: 369 GGDLLGSGTQSGPTPEAAGSLLELTAGGKQALTLPGGETRIFIQDGDTIIMRGSARRDGW 428

Query: 402 VRIGFGECRGKVLPA 416
            RIGFGE  G VLPA
Sbjct: 429 PRIGFGEVAGTVLPA 443


Lambda     K      H
   0.319    0.137    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: 549
Number of extensions: 25
Number of successful extensions: 9
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: 418
Length of database: 447
Length adjustment: 32
Effective length of query: 386
Effective length of database: 415
Effective search space:   160190
Effective search space used:   160190
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_050464693.1 AKL27_RS20355 (fumarylacetoacetase)
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))

# 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/TIGR01266.hmm
# target sequence database:        /tmp/gapView.25750.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01266  [M=420]
Accession:   TIGR01266
Description: fum_ac_acetase: fumarylacetoacetase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-170  551.8   0.0   5.7e-170  551.6   0.0    1.0  1  lcl|NCBI__GCF_001189915.1:WP_050464693.1  AKL27_RS20355 fumarylacetoacetas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001189915.1:WP_050464693.1  AKL27_RS20355 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.6   0.0  5.7e-170  5.7e-170       1     419 [.      15     443 ..      15     444 .. 0.95

  Alignments for each domain:
  == domain 1  score: 551.6 bits;  conditional E-value: 5.7e-170
                                 TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkadssr.rigvaiGdqildlskiaaaglfeglalkehq..e.vf 63 
                                               s+v++a+  + +fp+qnlPyG+f  + +s++ r gvaiGdqildl +++aag f    +++++  + ++
  lcl|NCBI__GCF_001189915.1:WP_050464693.1  15 SWVSSANadDNEFPIQNLPYGIFRRRGSSEQfRAGVAIGDQILDLRVAHAAGAFVAADAQTQAavHaAV 83 
                                               899998866899************7766544389********************987555444013146 PP

                                 TIGR01266  64 kestlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssi 132
                                                ++tln ++ l   a+ ++r  l +ll +++     ++al +  l+aq++a+  lPaqiGdytdfy+si
  lcl|NCBI__GCF_001189915.1:WP_050464693.1  84 AGATLNPLMDLDAGAWSALRLALSRLLRSDCSA--AQQALLTPCLVAQSDAEHALPAQIGDYTDFYTSI 150
                                               789*************************99988..77889999************************** PP

                                 TIGR01266 133 rhatnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlel 201
                                               +hat +G+lfr +dn+llPnyk++P+gyhGrass+ vsG + rrP Gq++a++a++Pvfgpck+ld+el
  lcl|NCBI__GCF_001189915.1:WP_050464693.1 151 HHATAIGKLFR-PDNPLLPNYKWVPIGYHGRASSIDVSGQQFRRPLGQTRAPDAEVPVFGPCKRLDYEL 218
                                               ***********.********************************************************* PP

                                 TIGR01266 202 elaffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsieal 270
                                               e+++f+g++n+lGea+p+ +ae h+fG++llndwsard+qawey+PlGPflak+fa+t+sPw+v++eal
  lcl|NCBI__GCF_001189915.1:WP_050464693.1 219 EVGVFIGNGNALGEAIPMANAEAHVFGLCLLNDWSARDMQAWEYQPLGPFLAKNFASTISPWIVTLEAL 287
                                               ********************************************************************* PP

                                 TIGR01266 271 ePfrvaqlePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnakslywtlkqq 333
                                                P+r   ++ + dp+plpyl +    ++ a+d++lev ++t  ++     ++++s sn+++ yw+++q 
  lcl|NCBI__GCF_001189915.1:WP_050464693.1 288 APYRAGWTRDSADPQPLPYLDDAGlrDHGALDVQLEVLIQTPAMRSaglaPHRLSLSNFRDSYWSVSQL 356
                                               ******9*************998555***************9999888889****************** PP

                                 TIGR01266 334 lahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckk 402
                                               +ahh+vnGcnlr GdllgsGt sG+ +ea Gsllel+a+Gk+++ l  getr f++dGd++i+rg +++
  lcl|NCBI__GCF_001189915.1:WP_050464693.1 357 VAHHTVNGCNLRGGDLLGSGTQSGPTPEAAGSLLELTAGGKQALTLPGGETRIFIQDGDTIIMRGSARR 425
                                               ********************************************************************* PP

                                 TIGR01266 403 eGvr.vGfGecaGkvlpa 419
                                               +G   +GfGe aG+vlpa
  lcl|NCBI__GCF_001189915.1:WP_050464693.1 426 DGWPrIGFGEVAGTVLPA 443
                                               **855************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (447 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: 9.86
//
[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 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