Alignments for a candidate for aldox-large in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Phaeobacter inhibens BS107

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate GFF1151 PGA1_c11660 molybdenum-containing hydroxylase

Query= metacyc::MONOMER-18071
         (749 letters)



>FitnessBrowser__Phaeo:GFF1151
          Length = 766

 Score =  343 bits (880), Expect = 2e-98
 Identities = 240/763 (31%), Positives = 378/763 (49%), Gaps = 36/763 (4%)

Query: 6   KPVKRIYDDKFVTGRSTYVDDIR-IPALYAGFVRSTYPHAIIKRIDVSDALKVNGIVAVF 64
           +PV+R+ D +F+TG+  Y++D   + AL A  +RS   H  I  +D+  A +  G+ A+ 
Sbjct: 9   QPVRRVEDIRFLTGQGRYLEDAAPVGALRAWVLRSPVAHGTITHLDLDMAREAEGVQAIL 68

Query: 65  T-----AKEINPLLKGGIRPWPTYIDIRSFRYS---ERKAFPENKVKYVGEPVAIVLGQD 116
           T     A  IN  + G +      +D R    +   ER     ++V++VGEP+A+V+ + 
Sbjct: 69  TLADLEAAGINVGMDGAV------VDNRDGSKAAAPERPMLVRDRVRFVGEPIAVVIAET 122

Query: 117 KYSVRDAIDKVVVEYEPLKPVIRMEEAEKDQVIIHEELKTNISYKIPF-KAGEVDKAFSE 175
               RDA + + ++ + L   + +    +    +H E   N ++          + AF+ 
Sbjct: 123 LEQARDAGEMIELDIDDLPAKVDLTAGGEQ---LHAEAPDNRAFDWSMGDEAATEAAFAS 179

Query: 176 SDKVVRVEAINERLIPNPMEPRGIVSRFEAGTLSIWYSTQVPHYMRSEFARILGIPESKI 235
           +   V ++  + R+I N MEPRG  + +  G L   Y  Q    M+ + +  LG+    +
Sbjct: 180 AAHRVALQVEDNRIIVNTMEPRGCFATWAEGRLQFTYGGQGVWAMKKQLSDKLGLASEAV 239

Query: 236 KVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLASEARHNVFT-GEV 294
            V+ PDVGG FG K    PE  AV  ++ +LG PV W + RSE ML+  A  ++ +  E+
Sbjct: 240 HVTTPDVGGGFGMKAMPYPEYFAVAHAARLLGGPVFWMSDRSEAMLSDNAGRDLTSLAEL 299

Query: 295 AVKRDGTILGIKGKLLLDLGAYIT-VTAGIQPLIIPMMIPGPYKIRNLDIESVAVYTNTP 353
           A   D  I G +     +LGAY +     +Q  +   ++ G Y I    +    +YTNT 
Sbjct: 300 AFDADLRITGYRVHSHCNLGAYNSHFGQPVQTQLFSRVLAGVYDIDTTWLRVEGIYTNTA 359

Query: 354 PITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVT--ELPYTNPFGLRYDSGD 411
            +  YRGA RPEA Y++ER+M   A ELG+D   +R +N +   + PY       YD GD
Sbjct: 360 QVDAYRGAGRPEAIYVLERVMDHAARELGVDPWELRRRNFIRADQFPYKTATDETYDVGD 419

Query: 412 YVGLLR--EGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGPWEYAEVRVDERG 469
           +  LL   E    L  +  +K A+  R  G+  GVGL YY+E     P E AEV  +E G
Sbjct: 420 FHQLLTLTEEAADLAGFAQRKAADALR--GNLRGVGLCYYIESILGDPSESAEVAFEEEG 477

Query: 470 DVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASMGTYGSRSVTIGG 529
            V +  GT  +GQG ET  AQ +AD   I  + + V+ GD+D +A   GT GSRSVT   
Sbjct: 478 RVSIYVGTQSNGQGHETVYAQFLADQTGIPAADITVVQGDSDRIAQGGGTGGSRSVTTQA 537

Query: 530 SAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSWDDVASIAYRSHD 589
           +A +   + +++      A    V    V ++  +F      +++ +  + A +A     
Sbjct: 538 NATLAAVDVMIEAFTPFLAEQLGVAPASVVFDGEQFSAPGS-NQRPTLVEAAEMARAQGR 596

Query: 590 PGLVEKIIYEN--DVTFPYGVHIATVEVD-DTGVARVLEYRAYDDIGKVVNPALAEAQIH 646
             L+           +FP G H+A + +D +TGV+ V  Y   DD G ++NP LAE Q+H
Sbjct: 597 HELLRHTARAKLPGRSFPNGAHVAEIVIDPETGVSHVDRYTVVDDFGNLINPLLAEGQVH 656

Query: 647 GGGVQAVGQALYEQALLNENGQLI-VTYADYYVPTAVEAPKFTSVFADQYHPSNYPTGSK 705
           GG  Q +GQAL E+ + + +GQL+  ++ DY +P A + P     FA      N P G K
Sbjct: 657 GGVAQGLGQALLERVVYDADGQLLTASFMDYALPRAADVPMIDVGFAPVPSTQN-PMGMK 715

Query: 706 GVGEAALIVGPAVIIRALEDAI---GTRFTKTPTTPEEILRAI 745
           G GEA  +   A +  A++DA+   G R  + P TP  +  A+
Sbjct: 716 GCGEAGTVGALAAVANAVQDAVWDRGVRQVEMPYTPLRLWEAL 758


Lambda     K      H
   0.317    0.136    0.394 

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: 1233
Number of extensions: 65
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: 749
Length of database: 766
Length adjustment: 40
Effective length of query: 709
Effective length of database: 726
Effective search space:   514734
Effective search space used:   514734
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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