GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Shewanella amazonensis SB2B

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__SB2B:6939342
          Length = 506

 Score =  207 bits (528), Expect = 6e-58
 Identities = 153/479 (31%), Positives = 236/479 (49%), Gaps = 34/479 (7%)

Query: 27  ATVSEYLGKDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAF 86
           A    ++G  +   + GE  +      +++P D + V  + +++     E A+ AA  A 
Sbjct: 17  ARYDNFIGGKWVPPVGGEYFD------NVSPVDGK-VFCQAARSDYRDIELALDAAHAAK 69

Query: 87  EEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYA 145
           + W  TS  ER+ +L + A +V +     + +   E GK   E  +AD    +D   Y+A
Sbjct: 70  DSWGKTSVTERSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFA 129

Query: 146 RQMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAP-IVTGNTVVL 204
              I   +G   +      + ++  P GV   I PWNF   +MA   +AP +  GN VVL
Sbjct: 130 G-CIRAQEGSAADLDANTVSYHLPEPLGVVGQIIPWNFPL-LMAAWKIAPALAAGNCVVL 187

Query: 205 KPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGT 264
           KPA  TP      +E +E+  LP GV+N V G GAE G  L    + + + FTGS EVG 
Sbjct: 188 KPAEQTPASIMVLLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGN 246

Query: 265 RIFERAAKVQPGQQHLKRVIAEMGGKDT------VVVDEDADIELAAQSIFTSAFGFAGQ 318
            I + AA      ++L     E+GGK        V+  ED  ++ A + +  + F   G+
Sbjct: 247 HILKCAA------ENLIPSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLAFFN-QGE 299

Query: 319 KCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIG 378
            C+  SR +V E +YD  +E+VI   ++     P   D  +G    +  YDKI+ Y++IG
Sbjct: 300 VCTCPSRVLVQESIYDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIG 359

Query: 379 KQEG-RLVSGG-----TGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDE 432
           + EG +++ GG      G +  GY+I+PTI    + K R+ QEEIFGPVV+     D  E
Sbjct: 360 RAEGAKVLMGGEFKLQDGPEKGGYYIQPTILKGHN-KMRVFQEEIFGPVVSVTTFKDEAE 418

Query: 433 ALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491
           AL +AN+T+YGL   V T +    +R  +    G ++   NC  A   +  FGG+K SG
Sbjct: 419 ALAIANDTQYGLGAGVWTRDMNLAQRMGRGIQAGRVWI--NCYHAYPAHAAFGGYKKSG 475


Lambda     K      H
   0.316    0.133    0.379 

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: 612
Number of extensions: 33
Number of successful extensions: 6
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: 515
Length of database: 506
Length adjustment: 35
Effective length of query: 480
Effective length of database: 471
Effective search space:   226080
Effective search space used:   226080
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