GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Burkholderia phytofirmans PsJN

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__BFirm:BPHYT_RS29875
          Length = 483

 Score =  380 bits (975), Expect = e-110
 Identities = 197/464 (42%), Positives = 282/464 (60%), Gaps = 4/464 (0%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74
           IDGK +P   G+   +INPATEE +  VA+G AA++D AV+AA+ AL   W  +   ER 
Sbjct: 14  IDGKRLPPGTGEYSVDINPATEEPIALVAQGSAADVDTAVRAARAALK-VWNGIRTAERA 72

Query: 75  AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQ 134
            +L ++  L+    EEL+ LESLD GKP       DIP A     +++ +   I  +   
Sbjct: 73  RILMRLAGLMRANLEELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKINGQVVP 132

Query: 135 MDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLA 194
           +   AL Y +R PVGV+  I PWN PL++  WK+APALA G T+++KPAE+TP+TA  + 
Sbjct: 133 VRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTALRIG 192

Query: 195 EICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRL 254
           E+  +AGVP GV+N+V G G    G AL  HP V+ ++FTG  + G+ I+  AA   KR+
Sbjct: 193 ELALEAGVPPGVLNIVTGKG-RVVGDALVAHPGVDKVTFTGSPSVGRGILQGAAGNFKRV 251

Query: 255 SYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAK 314
           + ELGGK+ N+IF D+NLD  +       F N G+VC  GSRI   R  Y+  +E+  A+
Sbjct: 252 TLELGGKSANLIFPDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAAR 311

Query: 315 TKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEP 374
            K + VGDP   +T +G LIS    + V GY++    EG +++TGG R    E+G+F+EP
Sbjct: 312 AKSIKVGDPSSRETSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVG--ERGFFVEP 369

Query: 375 TIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVA 434
           T+   +  + R+ +EEIFGPV +VI F+ E + +   N T Y L+A VW+ D+ R HRVA
Sbjct: 370 TVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHRVA 429

Query: 435 GQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478
             + AG VW+NT+   D+R P+GG   SG GRE G  + E ++E
Sbjct: 430 RDLRAGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENFTE 473


Lambda     K      H
   0.318    0.136    0.404 

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: 621
Number of extensions: 30
Number of successful extensions: 4
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: 486
Length of database: 483
Length adjustment: 34
Effective length of query: 452
Effective length of database: 449
Effective search space:   202948
Effective search space used:   202948
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: 52 (24.6 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:

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:

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:

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:

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