Aligments for a candidate for hcrA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for hcrA in Azospirillum brasilense Sp245

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate AZOBR_RS08560 AZOBR_RS08560 carbon-monoxide dehydrogenase

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__azobra:AZOBR_RS08560
          Length = 796

 Score =  298 bits (764), Expect = 6e-85
 Identities = 247/788 (31%), Positives = 361/788 (45%), Gaps = 70/788 (8%)

Query: 24  VTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIAVCTGAETPVP-FG 82
           +TG+  YT DI  P       +RSP+AHARI  ID + A    GVIAV TGA+      G
Sbjct: 20  LTGRGTYTDDINRPGQTHAVFVRSPYAHARITGIDAAEAMRAPGVIAVLTGADMEADKVG 79

Query: 83  VLPIAEN-------------EYPLARDKVRYRGDPVAAVAAIDEVTAEKALALIKVDYEV 129
            LP                  +P+ARD+ RY GD VA V A     A+ A  L+ VDYE 
Sbjct: 80  SLPCGWQIHSKDGSPMKEPPHFPIARDRARYVGDAVAVVIAETREQAKDAAELVMVDYEE 139

Query: 130 LPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAA---AFAEADLIREKTYTFAEV 186
           LPA +T   A++ GA  +HDD   N+  + H   GD AA   AF++A  + +       +
Sbjct: 140 LPAAVTSLKALEGGAPLVHDDVGGNLCFDWH--LGDAAAVDAAFSQAAHVAKLDLVNQRL 197

Query: 187 NHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CLQMDSARIRVIKPFLGGGF 245
               ME  A L EYD      TL TT+Q P+ + L + A  L +   ++RV+ P +GGGF
Sbjct: 198 VPNAMEPRAALGEYDRATGEHTLTTTSQNPHVIRLLMGAFVLGIPEHKLRVVAPDVGGGF 257

Query: 246 GARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAH-RGRPWTEVKMKIGLKKDGKIAA 304
           G++      E +    A+K    V+    R E+F+    GR       ++ + KDG   A
Sbjct: 258 GSKIFHYGEEAVVTWAAKKVGRPVKWTAERSESFLTDAHGRDHVS-HAELAMDKDGNFLA 316

Query: 305 LALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGHG 361
           L +      GAY       I T LY   L+ G Y  PAI  +   V+TNT P  A RG G
Sbjct: 317 LRVATIANMGAYLSTFAPSIPTYLYA-TLLAGQYKTPAIYAEVKAVFTNTVPVDAYRGAG 375

Query: 362 TVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQ--IPYVTMYAQRVMSYGVPECLEKVK 419
             +     E L+     E GID  ++R+ N +P   +PY T  A   + Y   +  + + 
Sbjct: 376 RPEACYLIERLVEVAAAETGIDKAELRRRNFVPASAMPYQTPVA---LQYDTGDFAKNLD 432

Query: 420 AA------SGWEERKGKLPK-GRGLGIALSHFVSGTS-TPKHWTGEPHATVNL------K 465
            A       G+  RK +  + G+  GI  + ++      P +  G   A   L      +
Sbjct: 433 IALPLVDYDGFAARKAESARRGKLRGIGFATYIEACGIAPSNVAGALGARAGLYESAEVR 492

Query: 466 LDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRV 525
               G +T+ TG+   GQG  T  +Q+ +E  GV +  + ++  D++  P   G+Y SR 
Sbjct: 493 FHPTGSVTVFTGSHSHGQGHETTFAQLVSERFGVPIENVEIVHGDTSKIPFGMGTYGSRS 552

Query: 526 TFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAA 585
             + G+A + A ++++    K AA  L+A E DIEV D  F+V+G+ D  L+  ++   A
Sbjct: 553 LAVGGSAIVKAMDKVERKAKKIAAHMLEAAEADIEVKDGRFVVAGT-DKALTIGDIALQA 611

Query: 586 MVDSGTITVKGTYTCPTEFQGDKKIRG---SAIGATMGFCY--AAQVVEASVDEITGKVT 640
            V             P  F  D+   G    A      F Y     V E  +D  TG V 
Sbjct: 612 YV-------------PHNFPLDELEPGLDEQAFYDPKNFTYPNGCHVCEVEIDPDTGVVQ 658

Query: 641 AHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVY--DNGRMVHGNILDYRVPT 698
                   D G+ +NPL VEGQ  GG+  G+GQAL E  VY  D+G+++ G+ +DY +P 
Sbjct: 659 VVNFAAVDDFGRVINPLIVEGQVHGGLVQGIGQALYENCVYDEDSGQLITGSYMDYCMPR 718

Query: 699 IVESPDIEVIIVESMD-PNGPFGAKEASEGMLAGFLPAIHEAVYEAV---GVRATDFPLS 754
             + P   V   E     + P G K   E    G   A+  AV  A+   GV   D P +
Sbjct: 719 ADDVPSFTVRYHEDQPCTHNPLGVKGCGEAGTIGASAAVMNAVVHALSEYGVTHLDMPAT 778

Query: 755 PDRITELL 762
           P+R+ + +
Sbjct: 779 PERVWQAI 786


Lambda     K      H
   0.317    0.134    0.386 

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: 1400
Number of extensions: 64
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: 769
Length of database: 796
Length adjustment: 41
Effective length of query: 728
Effective length of database: 755
Effective search space:   549640
Effective search space used:   549640
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 (21.7 bits)
S2: 55 (25.8 bits)

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, or view the source code.

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