Alignments for a candidate for astD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Burkholderia phytofirmans PsJN

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate BPHYT_RS25810 BPHYT_RS25810 aldehyde dehydrogenase

Query= reanno::SB2B:6938906
         (486 letters)



>FitnessBrowser__BFirm:BPHYT_RS25810
          Length = 796

 Score =  206 bits (523), Expect = 3e-57
 Identities = 150/456 (32%), Positives = 224/456 (49%), Gaps = 24/456 (5%)

Query: 4   FINGQWLA-GEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQ 62
           FI G W A   G+   S  PA GE + Q      A + AAV AAR AQ  W  LG  GR 
Sbjct: 36  FIGGAWHAPAAGERFASNAPATGEQLAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRA 95

Query: 63  AIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNE 122
             + A    ++ +    A + A + GKP  ET      ++ +  L  + + +   +E  +
Sbjct: 96  RHLYALARMVQRHSRLFAVLEALDNGKPIRETRDIDVPLVARHFLHHAGWAQLQESEFAD 155

Query: 123 GAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLK 182
            A         P GVV    P+NFP  +    I PA+  GN VV KP+E TP  A L  +
Sbjct: 156 YA---------PLGVVGQIVPWNFPLLMLAWKIAPAIATGNCVVLKPAEYTPLTALLFAE 206

Query: 183 LWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILAL 242
           L  +AGLPAGV+N+V G+  TG AL  HPQ+D + FTGS+  G L+    AG  GK L L
Sbjct: 207 LAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKIAFTGSTEVGRLIRSATAG-SGKSLTL 265

Query: 243 EMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAV 302
           E+GG +P IV   +D   A+  ++ + + + GQ C    RL V++G E  + +A L   +
Sbjct: 266 ELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVCCAGSRLLVQEGIEA-RFIAKLKRRM 324

Query: 303 KAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEM-----THLQAGTGL 357
           + ++VG  + D    +G+++        L+  ++L+  G +    +     T + +G   
Sbjct: 325 ETLRVGT-SLDKSIDLGAIVDPV----QLERIQSLVETGRREGCSVWQSPDTTIPSGGCF 379

Query: 358 VSPGLI-DVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYE 416
             P L+  V     L  EE FGP+L  + + + DEAI LAN++RYGL+A + ++      
Sbjct: 380 FPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALANNSRYGLAASVWSETIGRAL 439

Query: 417 YFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHR 452
               R+ +G+V W         A  FGG   SG  R
Sbjct: 440 DVAPRLASGVV-WINATNLFDAAVGFGGYRESGYGR 474



 Score = 61.2 bits (147), Expect = 1e-13
 Identities = 53/213 (24%), Positives = 85/213 (39%), Gaps = 2/213 (0%)

Query: 24  NGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQAIVEAYRNELEANKAELAEVI 83
           +G  + +  A     ++ AV AAR AQ +W       R  ++      L     E    +
Sbjct: 545 DGTPVGEVAAGNRKDIRNAVEAARAAQ-KWSQASTHNRAQVLFYLAENLAVRADEFVRQL 603

Query: 84  AQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNEGAAGRAVLRHKPHGVVAVFGP 143
               G        E  A + ++    +   K  G        G A+  H+P GV+ +  P
Sbjct: 604 VVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGIACP 663

Query: 144 YNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLKLWEKAGLPAGVINLVQGE-VE 202
              P         PAL  GN VV  PSE +P       ++ E + +P GV+N+V GE   
Sbjct: 664 DEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVTGERGA 723

Query: 203 TGKALASHPQLDGLFFTGSSRTGHLLHQQYAGH 235
              AL  H  +D ++  GS+    L+ ++  G+
Sbjct: 724 LLPALVKHDDVDAVWCFGSAADSTLVERESVGN 756


Lambda     K      H
   0.317    0.133    0.393 

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: 898
Number of extensions: 55
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 486
Length of database: 796
Length adjustment: 37
Effective length of query: 449
Effective length of database: 759
Effective search space:   340791
Effective search space used:   340791
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 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. 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 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