Alignments for a candidate for fahA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Herbaspirillum seropedicae SmR1

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate HSERO_RS05610 HSERO_RS05610 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>FitnessBrowser__HerbieS:HSERO_RS05610
          Length = 448

 Score =  380 bits (977), Expect = e-110
 Identities = 205/427 (48%), Positives = 268/427 (62%), Gaps = 25/427 (5%)

Query: 7   AEDSDFPIHNLPYGVFSTRGDPRP-RIGVAIGDQILDLSIIKHL--FTGPVLSKHQDVF- 62
           A+   FPI NLPYGVF   G     R+GVAIGDQILDL   +    F+G   +  Q    
Sbjct: 25  ADGCPFPIQNLPYGVFRRAGSEEDFRVGVAIGDQILDLPAAQSAGAFSGFDEATRQAAHA 84

Query: 63  --NQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPAT 120
             +   LN+ M L  A+W   R+ L +LL  +       TEL  C  + QA A   +PA 
Sbjct: 85  ACSGSRLNALMALTPASWSALRLALSHLLRTASPH---QTELAAC-LVPQAQAEYDVPAA 140

Query: 121 IGDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQM 180
           IGDYTDFY+S  HAT VG +FR  +N L+PN+  +P+GYHGR SS+ VSG   RRP+GQ 
Sbjct: 141 IGDYTDFYTSIHHATTVGKLFRP-DNPLLPNYKWVPIGYHGRVSSIAVSGQQFRRPLGQT 199

Query: 181 KPDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQ 240
           K  D+  P +G CK LD ELE+  F+G GN +GEP+P+ +A + +FG+ L+NDWSARD+Q
Sbjct: 200 KAPDADAPTFGPCKRLDYELEIGIFIGGGNAMGEPVPMEEAEDKVFGLCLLNDWSARDVQ 259

Query: 241 KWEYVPLGPFLGKSFGTTVSPWVVPMDALMPF--AVPNPKQDPRPLPYLCHDEPY----- 293
            WEY PLGPFL KSF +T+SPW+V ++AL P+  +   P  DP+PLPYL  D P      
Sbjct: 260 AWEYQPLGPFLSKSFASTISPWIVTLEALAPYRCSWSRPDGDPQPLPYL--DAPTLRTQG 317

Query: 294 TFDINLSVNLKGEGMSQAA----TICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASG 349
            FD+ L V ++   M QA      +  SN++  YWT+ Q +THH+VNGCNLRPGD L SG
Sbjct: 318 AFDVQLEVLIQTAAMRQAGQPPQRLSLSNYRDAYWTVAQLVTHHTVNGCNLRPGDFLGSG 377

Query: 350 TISGPEPENFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGY-RIGFGQC 408
           T+SGP P+  GS+LEL+  G  P+ L +G+ R FL DGD +I+    + DG   IGFG+ 
Sbjct: 378 TLSGPAPDEAGSLLELTTGGKSPLTLASGEKRVFLEDGDTIILRAVARRDGLPLIGFGES 437

Query: 409 AGKVLPA 415
           AG VLPA
Sbjct: 438 AGTVLPA 444


Lambda     K      H
   0.321    0.139    0.440 

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: 621
Number of extensions: 33
Number of successful extensions: 8
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: 419
Length of database: 448
Length adjustment: 32
Effective length of query: 387
Effective length of database: 416
Effective search space:   160992
Effective search space used:   160992
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 HSERO_RS05610 HSERO_RS05610 (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.26274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.3e-172  557.7   0.0   9.4e-172  557.5   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05610  HSERO_RS05610 fumarylacetoacetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05610  HSERO_RS05610 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  557.5   0.0  9.4e-172  9.4e-172       1     419 [.      18     444 ..      18     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 557.5 bits;  conditional E-value: 9.4e-172
                                  TIGR01266   1 sfvavak..nsdfplqnlPyGvfstk.adssrrigvaiGdqildlskiaaaglfegl...alkehqev 62 
                                                s+v++a+   ++fp+qnlPyGvf    ++ + r+gvaiGdqildl ++++ag f+g    + ++++ +
  lcl|FitnessBrowser__HerbieS:HSERO_RS05610  18 SWVPSANadGCPFPIQNLPYGVFRRAgSEEDFRVGVAIGDQILDLPAAQSAGAFSGFdeaTRQAAHAA 85 
                                                899998864689***********8431455679*******************9998755234455567 PP

                                  TIGR01266  63 fkestlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfys 130
                                                 ++s lna++al+ +++ ++r  l +ll + +      +++    l++qa+a+  +Pa iGdytdfy+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05610  86 CSGSRLNALMALTPASWSALRLALSHLLRTASPH----QTELAACLVPQAQAEYDVPAAIGDYTDFYT 149
                                                8999************************954444....5667789*********************** PP

                                  TIGR01266 131 sirhatnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkld 198
                                                si+hat vG+lfr +dn+llPnyk++P+gyhGr ss+ vsG + rrP Gq+ka++a+ P+fgpck+ld
  lcl|FitnessBrowser__HerbieS:HSERO_RS05610 150 SIHHATTVGKLFR-PDNPLLPNYKWVPIGYHGRVSSIAVSGQQFRRPLGQTKAPDADAPTFGPCKRLD 216
                                                *************.****************************************************** PP

                                  TIGR01266 199 lelelaffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvs 266
                                                +ele+++f+g +n++Ge+vp+e ae+++fG++llndwsard+qawey+PlGPfl+ksfa+t+sPw+v+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05610 217 YELEIGIFIGGGNAMGEPVPMEEAEDKVFGLCLLNDWSARDVQAWEYQPLGPFLSKSFASTISPWIVT 284
                                                ******************************************************************** PP

                                  TIGR01266 267 iealePfrvaqlePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnakslyw 328
                                                +eal P+r +  +P++dp+plpyl       + afd++lev ++t+ +++    ++++s sn ++ yw
  lcl|FitnessBrowser__HerbieS:HSERO_RS05610 285 LEALAPYRCSWSRPDGDPQPLPYLDAPTlrTQGAFDVQLEVLIQTAAMRQagqpPQRLSLSNYRDAYW 352
                                                ************************98755599****************9999999************* PP

                                  TIGR01266 329 tlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevil 396
                                                t++q ++hh+vnGcnlr+Gd+lgsGt+sG+ +++ Gsllel+++Gk ++ la+ge+r fledGd++il
  lcl|FitnessBrowser__HerbieS:HSERO_RS05610 353 TVAQLVTHHTVNGCNLRPGDFLGSGTLSGPAPDEAGSLLELTTGGKSPLTLASGEKRVFLEDGDTIIL 420
                                                ******************************************************************** PP

                                  TIGR01266 397 rgvckkeGvr.vGfGecaGkvlpa 419
                                                r+v++++G   +GfGe aG+vlpa
  lcl|FitnessBrowser__HerbieS:HSERO_RS05610 421 RAVARRDGLPlIGFGESAGTVLPA 444
                                                ********987************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (448 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.66
//
[ok]

This GapMind analysis is from Sep 17 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