GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Klebsiella michiganensis M5al

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase

Query= BRENDA::Q9RW56
         (523 letters)



>FitnessBrowser__Koxy:BWI76_RS12820
          Length = 499

 Score =  238 bits (608), Expect = 3e-67
 Identities = 169/516 (32%), Positives = 262/516 (50%), Gaps = 38/516 (7%)

Query: 25  QAALAKVRKELLGKHYPLIIDG--QEVDTEGKIQSINPCDTSEVVGTTAKATIGDAENAL 82
           Q AL    ++ L + + L +DG  Q  ++E ++   NP  T + + +TA A   D + A+
Sbjct: 5   QVALLASVQQFLDRQHGLYLDGTQQAAESEQRLTVWNPA-TGQAIASTADANAADVDRAV 63

Query: 83  QGAWKAF--ESWKKWDMDARARILLKAAAILKRRRLEACALMSIEVGK--NYAEADVEVA 138
             AW+AF   SW       R RILL+ A ++++   E   L ++E GK  N + A  EV 
Sbjct: 64  MSAWRAFVSRSWAGRTPADRERILLRFADLVEQHGEELAQLETLEQGKSINISRA-FEVG 122

Query: 139 EAIDFLEYYARSAMKYAG----------FGSSETTWFEGEENGLMSIPLGVGVSISPWNF 188
             ++++ Y A    K +G           G     W + E       P+GV   I PWNF
Sbjct: 123 CTLNWMRYTAGLTTKISGRTLDVSIPFPAGGRYQAWTKKE-------PVGVVAGIVPWNF 175

Query: 189 PCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGE 248
           P  I +      + AG  +V+KP+E   L    + ++  EAG+P GV   + G G   G 
Sbjct: 176 PLMIGMWKVMPALAAGCSIVIKPSETTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGA 235

Query: 249 YLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELGGKDGLIVDETADIEN 308
            LT+H     ++FTGS A G  I  VAA        + RV +ELGGK+  IV + AD + 
Sbjct: 236 ALTSHPLVAKVSFTGSTATGKQIARVAA------DRLTRVTLELGGKNPAIVLKDADPQW 289

Query: 309 AITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAKALKMGTGE-ENANVTAVV 367
            I     G+F   GQ C+A SR+ +   ++D +V+GF +  K+L++G G  E++ +  VV
Sbjct: 290 VIEGLMTGSFLNQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMLESSQINPVV 349

Query: 368 NQMSFNKIKGYLELAPSEGKVLLGGEATGEANGKQGYYIQPTIVGDVDRNSRLAQEEIFG 427
           +Q    K+  YL+ A  +   L+ G A  +A   QGYYI PT+V + D   RL +EE+FG
Sbjct: 350 SQAHCAKVAAYLDEARQQKAELISGHAGPDA---QGYYIAPTLVINPDAGLRLCREEVFG 406

Query: 428 PVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEFEVGNLYFNRKITGAIV 487
           PVV ++R  D ++AL +AN +++GLT  V +    +        + G ++ N      I 
Sbjct: 407 PVVNLVRVADGEEALLLANDSDFGLTASVWTRDLTQALSYTDRLQAGTVWVNSHT--LID 464

Query: 488 GVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTVTERW 523
              PFGG   SGT  +  GPD+L ++ + K+V  R+
Sbjct: 465 ANLPFGGMKQSGT-GRDFGPDWLDDWCETKSVCVRY 499


Lambda     K      H
   0.317    0.134    0.391 

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: 595
Number of extensions: 21
Number of successful extensions: 5
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: 523
Length of database: 499
Length adjustment: 35
Effective length of query: 488
Effective length of database: 464
Effective search space:   226432
Effective search space used:   226432
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: 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