Alignments for a candidate for fahA in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Rhodococcus qingshengii djl-6-2

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_003940530.1 C1M55_RS23760 fumarylacetoacetase

Query= BRENDA::Q94272
         (418 letters)



>NCBI__GCF_002893965.1:WP_003940530.1
          Length = 396

 Score =  367 bits (943), Expect = e-106
 Identities = 193/413 (46%), Positives = 261/413 (63%), Gaps = 28/413 (6%)

Query: 5   VSVPQNSDFPIQNLPYGVFSTKADSSRHIGVAIGDQILNLAEIANLFDGPQLKAHQDVFK 64
           + +P +S F + NLPYGVFS      R +GV + + +++LA  A L D         VF 
Sbjct: 6   IDIPADSLFGLDNLPYGVFSPAGGLPR-VGVRVAESVVDLA--ATLGDS--------VFS 54

Query: 65  QSTLNAFMALPRPAWLEARARIQQLLSEDCAVLRDNAHLRSRALVAQSDATMHLPAQIGD 124
           + TLNAFMA  R  W+  R RI +L++ +         + S A+ +    TMHLP  + D
Sbjct: 55  EPTLNAFMAQGRDQWVSVRNRITELVTSE---------IDSNAVFSVDSVTMHLPIAVAD 105

Query: 125 YTDFYSSIHHATNVGIMFRGKENALMPNWKWLPVGYHGRASSIVVSGTDLKRPVGQTKAP 184
           Y DFY+S +HATN+G +FR     LMPNWK LPVGYHGR+S+IVVSGTD+ RP GQ KAP
Sbjct: 106 YVDFYASENHATNLGRLFRPDAAPLMPNWKHLPVGYHGRSSTIVVSGTDIVRPCGQRKAP 165

Query: 185 DAEVPSFGPSKLMDFELEMAFFVGGPENELGTRVPIEKAEDRIFGVVLMNDWSARDIQAW 244
           D E P FGPS+ +D E EM F VG P +++G  +  ++  + +FG V++NDWSARDIQAW
Sbjct: 166 DQESPDFGPSRRLDIEAEMGFIVGTP-SKMGDSITPDEFAEYVFGAVVVNDWSARDIQAW 224

Query: 245 EYVPLGPFLAKSFATTVSPWVVSIEALRPYFVENPVQDPVPPAYLHHDDPFTLDINLAVS 304
           EYVPLGP L KSFAT++SPWVV + AL    ++ PVQDP P +YL  ++ + LDI+LAV 
Sbjct: 225 EYVPLGPNLGKSFATSISPWVVPLLALEAARIDTPVQDPEPLSYLRGEEKWGLDIDLAVE 284

Query: 305 IRPEGDAVDHIVCKTNFKHLYWTLKQQLAHHTVNGCNLRAGDLLGSGTVSGPEEGAYGSM 364
                    H+V +  +  +YW+  Q LAH T+NG     GDL  SGT+SGP++   G+ 
Sbjct: 285 WN------GHVVSRPPYAQMYWSPAQMLAHTTINGAAASTGDLFASGTISGPDKDQRGAF 338

Query: 365 LELSWRGAKEVPVGSEIRKFLKDGDEVNLSGVCE-KNGVRIGFGECRGKVLPA 416
           +EL+W G + V VGSE R FL+DGD + +S       G RIGFG+   ++LPA
Sbjct: 339 IELTWGGKEPVAVGSETRTFLEDGDTIAISATAPGVGGSRIGFGDVHARILPA 391


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: 496
Number of extensions: 19
Number of successful extensions: 6
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: 396
Length adjustment: 31
Effective length of query: 387
Effective length of database: 365
Effective search space:   141255
Effective search space used:   141255
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: 50 (23.9 bits)

Align candidate WP_003940530.1 C1M55_RS23760 (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.3763003.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-135  438.6   0.0   1.7e-135  438.1   0.0    1.2  1  NCBI__GCF_002893965.1:WP_003940530.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_003940530.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.1   0.0  1.7e-135  1.7e-135       3     419 ..       6     391 ..       4     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 438.1 bits;  conditional E-value: 1.7e-135
                             TIGR01266   3 vavaknsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflalg 75 
                                           ++++ +s f l+nlPyGvfs  a+  +r+gv + ++++dl++ +               vf+e tlnaf+a g
  NCBI__GCF_002893965.1:WP_003940530.1   6 IDIPADSLFGLDNLPYGVFS-PAGGLPRVGVRVAESVVDLAATLG------------DSVFSEPTLNAFMAQG 65 
                                           78999***************.88999**************98776............469999********** PP

                             TIGR01266  76 rparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdna 148
                                           r  ++ vr+r+ +l++         +++ ++a+ +  ++tmhlP+ + dy dfy+s +hatn+G lfr    +
  NCBI__GCF_002893965.1:WP_003940530.1  66 RDQWVSVRNRITELVT---------SEIDSNAVFSVDSVTMHLPIAVADYVDFYASENHATNLGRLFRPDAAP 129
                                           **************99.........345678999**********************************99999 PP

                             TIGR01266 149 llPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpiek 221
                                           l+Pn+khlPvgyhGr+s++vvsGt++ rP Gq ka++ + P fgp+++ld+e e++f vgt+ ++G+++  + 
  NCBI__GCF_002893965.1:WP_003940530.1 130 LMPNWKHLPVGYHGRSSTIVVSGTDIVRPCGQRKAPDQESPDFGPSRRLDIEAEMGFIVGTPSKMGDSITPDE 202
                                           ************************************************************************* PP

                             TIGR01266 222 aeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaqlePeqdpkplpylredr 294
                                            +e +fG v++ndwsardiqaweyvPlGP l+ksfat++sPwvv++ ale  r+    P+qdp+pl+ylr + 
  NCBI__GCF_002893965.1:WP_003940530.1 203 FAEYVFGAVVVNDWSARDIQAWEYVPLGPNLGKSFATSISPWVVPLLALEAARID--TPVQDPEPLSYLRGE- 272
                                           *****************************************************99..9*************9. PP

                             TIGR01266 295 adtafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsll 367
                                           ++  +di+l+v+   +G    +v+sr    ++yw+ +q+lah ++nG    +Gdl++sGtisG+++++ G+++
  NCBI__GCF_002893965.1:WP_003940530.1 273 EKWGLDIDLAVEW--NG----HVVSRPPYAQMYWSPAQMLAHTTINGAAASTGDLFASGTISGPDKDQRGAFI 339
                                           99*******9986..45....89************************************************** PP

                             TIGR01266 368 elsakGkkevkladgetrkfledGdevilrgvckk.eGvrvGfGecaGkvlpa 419
                                           el+++Gk++v ++ +etr+fledGd++ +++++    G r+GfG+   ++lpa
  NCBI__GCF_002893965.1:WP_003940530.1 340 ELTWGGKEPVAVG-SETRTFLEDGDTIAISATAPGvGGSRIGFGDVHARILPA 391
                                           *************.9****************996526788************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (396 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.00
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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