Alignments for a candidate for fahA in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Azohydromonas australica DSM 1124

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_028999960.1 H537_RS0124565 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>NCBI__GCF_000430725.1:WP_028999960.1
          Length = 434

 Score =  391 bits (1004), Expect = e-113
 Identities = 204/416 (49%), Positives = 274/416 (65%), Gaps = 18/416 (4%)

Query: 9   DSDFPIHNLPYGVFSTRGDPRP-RIGVAIGDQILDLSIIKH--LFTGPVLSKHQDVFNQP 65
           D+DFPI NLP+ VF  +G     R GVAIGDQI+DL+ +    LF G    +      Q 
Sbjct: 22  DTDFPIQNLPFAVFRRKGSSEAFRGGVAIGDQIVDLAAVSAAGLFDGAA-GEAVAAAAQG 80

Query: 66  TLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATIGDYT 125
            LN+ M LGQ AW+  R+ L   L    A+      L+ C  + Q  A   +PA IGDYT
Sbjct: 81  KLNALMALGQPAWRALRLALSRALRDGAAQ---QPRLQAC-LVPQVEAQYDVPARIGDYT 136

Query: 126 DFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPDDS 185
           DFY+S  HATN+G +FR  +N LMPN+  +P+GYHGR+SS+ VSG   RRP+GQ  P  +
Sbjct: 137 DFYTSVHHATNIGRLFRP-DNPLMPNYKWVPIGYHGRSSSIAVSGQVFRRPVGQTLPAGA 195

Query: 186 KPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWEYV 245
             PV G  + LD+ELE+  F+G GN LGEP+ I +A +H+FG+ L+NDWSARDIQ WEY 
Sbjct: 196 TQPVTGPSQRLDIELELGIFIGSGNSLGEPVAIEQAEDHVFGICLLNDWSARDIQAWEYQ 255

Query: 246 PLGPFLGKSFGTTVSPWVVPMDALMPFAVP--NPKQDPRPLPYL---CHDEPYTFDINLS 300
           PLGPF+ K+F TT+SPW+V +DAL P+ VP   P+ DP+PLPYL    +    + DI L 
Sbjct: 256 PLGPFMSKNFATTISPWIVTLDALAPYRVPFQRPEGDPQPLPYLDSEANRREGSLDIQLQ 315

Query: 301 VNLKGEGMSQA---ATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPE 357
           V+L    + +A   ATIC++++++ YWT+ Q + HH+VNGCNL+PGDL  SGT+SGP  +
Sbjct: 316 VDLLTPRLREAGSVATICRTSYRHAYWTVAQMVAHHTVNGCNLQPGDLFGSGTLSGPTLD 375

Query: 358 NFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDG-YRIGFGQCAGKV 412
             G+++EL+  G +P+ L +G+TR FL DGD VII G+C+  G  RIGFGQC G V
Sbjct: 376 QAGALIELTSGGKQPLQLPDGETRTFLQDGDSVIIRGWCKKPGAARIGFGQCMGTV 431


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: 610
Number of extensions: 38
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: 434
Length adjustment: 32
Effective length of query: 387
Effective length of database: 402
Effective search space:   155574
Effective search space used:   155574
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_028999960.1 H537_RS0124565 (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.20458.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-176  571.5   0.0   6.1e-176  571.3   0.0    1.0  1  lcl|NCBI__GCF_000430725.1:WP_028999960.1  H537_RS0124565 fumarylacetoaceta


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000430725.1:WP_028999960.1  H537_RS0124565 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.3   0.0  6.1e-176  6.1e-176       1     418 [.      13     433 ..      13     434 .] 0.94

  Alignments for each domain:
  == domain 1  score: 571.3 bits;  conditional E-value: 6.1e-176
                                 TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkadssr.rigvaiGdqildlskiaaaglfeglalkehqevfkes 66 
                                               s+v++a+  ++dfp+qnlP+ vf  k +s+  r gvaiGdqi+dl+++ aaglf+g a++e+  +  ++
  lcl|NCBI__GCF_000430725.1:WP_028999960.1  13 SWVDSANypDTDFPIQNLPFAVFRRKGSSEAfRGGVAIGDQIVDLAAVSAAGLFDG-AAGEAVAAAAQG 80 
                                               89***99999*************966554433789*********************.9999******** PP

                                 TIGR01266  67 tlnaflalgrparkevrerlqkllsesaevlrdnaalrke...allaqaeatmhlPaqiGdytdfyssi 132
                                                lna++alg+pa++++r  l +        lrd aa++++    l++q ea+  +Pa+iGdytdfy+s+
  lcl|NCBI__GCF_000430725.1:WP_028999960.1  81 KLNALMALGQPAWRALRLALSRA-------LRDGAAQQPRlqaCLVPQVEAQYDVPARIGDYTDFYTSV 142
                                               *****************887655.......566666655422169************************ PP

                                 TIGR01266 133 rhatnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlel 201
                                               +hatn+G lfr +dn+l+Pnyk++P+gyhGr+ss+ vsG   rrPvGq+++++a +Pv gp+++ld+el
  lcl|NCBI__GCF_000430725.1:WP_028999960.1 143 HHATNIGRLFR-PDNPLMPNYKWVPIGYHGRSSSIAVSGQVFRRPVGQTLPAGATQPVTGPSQRLDIEL 210
                                               ***********.********************************************************* PP

                                 TIGR01266 202 elaffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsieal 270
                                               el++f+g++n+lGe+v ie+ae+h+fG++llndwsardiqawey+PlGPf++k+fatt+sPw+v+++al
  lcl|NCBI__GCF_000430725.1:WP_028999960.1 211 ELGIFIGSGNSLGEPVAIEQAEDHVFGICLLNDWSARDIQAWEYQPLGPFMSKNFATTISPWIVTLDAL 279
                                               ********************************************************************* PP

                                 TIGR01266 271 ePfrvaqlePeqdpkplpylredr..adtafdielevslkteGlae...aavisrsnakslywtlkqql 334
                                                P+rv+  +Pe+dp+plpyl  +    + ++di+l+v+l t  l+e    a+i+r+  ++ ywt++q++
  lcl|NCBI__GCF_000430725.1:WP_028999960.1 280 APYRVPFQRPEGDPQPLPYLDSEAnrREGSLDIQLQVDLLTPRLREagsVATICRTSYRHAYWTVAQMV 348
                                               ********************876434899**********9998888655789***************** PP

                                 TIGR01266 335 ahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckke 403
                                               ahh+vnGcnl++Gdl+gsGt+sG+  ++ G+l+el+ +Gk++++l dgetr+fl+dGd vi+rg ckk 
  lcl|NCBI__GCF_000430725.1:WP_028999960.1 349 AHHTVNGCNLQPGDLFGSGTLSGPTLDQAGALIELTSGGKQPLQLPDGETRTFLQDGDSVIIRGWCKKP 417
                                               ********************************************************************* PP

                                 TIGR01266 404 Gvr.vGfGecaGkvlp 418
                                               G   +GfG+c G+v +
  lcl|NCBI__GCF_000430725.1:WP_028999960.1 418 GAArIGFGQCMGTVTA 433
                                               *877*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (434 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: 7.67
//
[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