GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Phaeobacter inhibens BS107

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate GFF3775 PGA1_262p01790 aldehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>FitnessBrowser__Phaeo:GFF3775
          Length = 483

 Score =  256 bits (654), Expect = 1e-72
 Identities = 151/450 (33%), Positives = 233/450 (51%), Gaps = 12/450 (2%)

Query: 41  INGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAV 100
           I G+ V    +I + NP+D  +++G  ++AS +  +  ++ A +A  EW     E +  V
Sbjct: 9   IAGDWVAGATEIENRNPSDLNDLIGMFAQASPDQLDATLEQAQRAQVEWAGYGIERKYNV 68

Query: 101 LFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSR 160
           L     ++  R  E   LL +E GKP  E   +   A  F  YYA + +        + R
Sbjct: 69  LMAIGTEMMTRAEELGTLLAREEGKPLAEGKGEVYRAGQFFTYYAAETLRQMGDTADSVR 128

Query: 161 EGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEV 220
           +G +      P GV VVI PWNF  A  +      +  GN VV KPA+ TP  A   VE+
Sbjct: 129 DGIEIDVRREPVGVVVVISPWNFPTATASWKIAPALCYGNAVVWKPANVTPASAVALVEI 188

Query: 221 LEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQHL 280
           +    +PKG+V+ V G+G+ +G  LV+ PK + I+FTGS  VG  I   A       Q+L
Sbjct: 189 IARQDIPKGLVSLVMGAGSSIGQRLVESPKVNAISFTGSVPVGKGIAACAI------QNL 242

Query: 281 KRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERV 340
            RV  EMG K+ + V +DADI+LA       AFG +GQKC+A SR VVH+ ++DQ +E++
Sbjct: 243 TRVQMEMGSKNALAVMDDADIDLAVSLALGGAFGGSGQKCTASSRLVVHQSIHDQFVEKL 302

Query: 341 IEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD--SKGYF 397
           +   ++        A   MGPV+ +   ++ ++Y+++   EG  L+ GG   +  + GY+
Sbjct: 303 VMGAKAMKVGHALEAGTQMGPVVSEQQLNENLAYVDLAASEGAELLCGGQRLEMATDGYY 362

Query: 398 IKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIE 457
           + P IF   +   R+ +EE+F P+     V+ +DEAL V N+T +GLT  ++T N     
Sbjct: 363 VSPGIFVGTNNDMRINREEMFAPLACVIPVASYDEALHVVNDTNFGLTAGIVTTNLARAT 422

Query: 458 RAKQEFHVGNLYFNRNCTGAIVGYH-PFGG 486
             ++    G +  N    G    YH PFGG
Sbjct: 423 HFRRNAQSGCVMVNLPTAG--TDYHVPFGG 450


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: 576
Number of extensions: 23
Number of successful extensions: 3
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: 483
Length adjustment: 34
Effective length of query: 481
Effective length of database: 449
Effective search space:   215969
Effective search space used:   215969
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