Alignments for a candidate for praB in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for praB in Sinorhizobium medicae WSM419

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_012061562.1 SMED_RS23160 aldehyde dehydrogenase family protein

Query= BRENDA::Q1XGK8
         (486 letters)



>NCBI__GCF_000017145.1:WP_012061562.1
          Length = 794

 Score =  327 bits (839), Expect = 7e-94
 Identities = 189/464 (40%), Positives = 261/464 (56%), Gaps = 22/464 (4%)

Query: 6   HFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAE 65
           HFINGAFV + SG+TF+   P+ G ++  +   GR +VDAAV AAR A +GPW KLS   
Sbjct: 35  HFINGAFVAAVSGKTFDTFEPATGALLAGIARGGREDVDAAVAAARKA-QGPWAKLSGHA 93

Query: 66  RAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEA 125
           RA  L+ +A  I          E LD GKP      ID+P  A +F   A   +    E 
Sbjct: 94  RARHLYALARLIQRHARLIAVVEALDNGKPIRETRDIDVPLAARHFYHHAGWAQLQETE- 152

Query: 126 FEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPL 185
                        +A + P GV+G + PWN P L++ WKV PALA GNTV++KP+E TPL
Sbjct: 153 -------------FADQVPVGVVGQVIPWNFPFLMLAWKVAPALALGNTVILKPAEYTPL 199

Query: 186 TATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAA 245
           TA L  E+  A+G+P GV NVV G G    GA + EH D+D   FTG T  G +I    A
Sbjct: 200 TALLFAEMAAASGLPPGVLNVVTGEG--ETGALIVEHEDIDKIAFTGSTEIGRLIREKTA 257

Query: 246 KGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEFV 305
              + ++LELGGK+  IVF D D+D A+EG + + + N GQVC    R+ V+  +   F 
Sbjct: 258 GSGKSLTLELGGKSPFIVFDDADIDAAVEGVVDAIWFNQGQVCCAGSRLLVQEGVAPVFH 317

Query: 306 ARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPAH 365
            RLK   ++L +G P D S +   +V+    +++     + V +G S+       ++P  
Sbjct: 318 ERLKRRMDTLRVGHPLDKSIDMAAIVAPVQLQRIAELVAKGVAEGASMHQPR--IELPK- 374

Query: 366 LAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWTE 425
             GG++ +PT+ TG+   S V TEEIFGP      F T +EAI+LAN   YGLA+++W+E
Sbjct: 375 --GGSFYRPTLLTGVQPTSVVATEEIFGPVAVSMTFRTPDEAIQLANHSRYGLAASVWSE 432

Query: 426 NGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGG 469
               A  VA ++ AG+VWVN+  L D    FGG ++SG GREGG
Sbjct: 433 TIGLALHVAAKLAAGVVWVNATNLFDAAAGFGGKRESGFGREGG 476



 Score =  100 bits (250), Expect = 1e-25
 Identities = 77/255 (30%), Positives = 123/255 (48%), Gaps = 15/255 (5%)

Query: 5   KHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVA 64
           K FI+G       G     +    G+V+G V E  R ++  AV AAR A    W   +  
Sbjct: 520 KLFIDGK-QARPDGNYSRPVLSPKGKVVGEVGEGNRKDIRNAVVAARGA--SGWSSATAH 576

Query: 65  ERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAA---NFKVFADLLKNV 121
            RA+IL+ +A+ +++R  EF +     TG   + ++  ++    A   ++  +AD  + V
Sbjct: 577 NRAQILYYIAENLSSRGAEFADRIAAMTGA-SAASARTEVEASIARLFSYGAWADKYEGV 635

Query: 122 ANEAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSE 181
            ++      P   G +  A+  P+GV+GVI P   PLL +   V P +A GN V+  PSE
Sbjct: 636 VHQ------PPLRG-VALAMPEPQGVVGVICPPEAPLLGLVSLVAPLIAVGNRVIAVPSE 688

Query: 182 ETPLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIM 241
             PL AT    V++ + VP GV N+V G   + A A L  H DVDA    G      ++ 
Sbjct: 689 THPLAATDFYSVLETSDVPPGVINIVTGLATELAKA-LAAHNDVDALWAFGSPELSTLVE 747

Query: 242 RAAAKGVRQVSLELG 256
           R +   +++  ++ G
Sbjct: 748 RLSIGNLKRTFVDYG 762


Lambda     K      H
   0.318    0.136    0.411 

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: 1027
Number of extensions: 51
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 486
Length of database: 794
Length adjustment: 37
Effective length of query: 449
Effective length of database: 757
Effective search space:   339893
Effective search space used:   339893
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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