GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Sinorhizobium meliloti 1021

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate SM_b20891 SM_b20891 dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>lcl|FitnessBrowser__Smeli:SM_b20891 SM_b20891 dehydrogenase
          Length = 477

 Score =  283 bits (725), Expect = 7e-81
 Identities = 171/475 (36%), Positives = 254/475 (53%), Gaps = 13/475 (2%)

Query: 40  VINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99
           +I GE V  +  + +INP++ ++VVG  ++AS E A+ AI AA  AF  W  +   ER A
Sbjct: 7   LIAGEWVGGDG-VANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHA 65

Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159
           +L + A ++  RK E   LL +E GK   E   +T  A    E++A + + LA     + 
Sbjct: 66  ILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSV 125

Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219
           R G   +    P GV  +I PWNF  AI A      +  GNT+V KPA   P  +   V+
Sbjct: 126 RPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVD 185

Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279
           +L  +GLPKGV+N V G G+ VG  ++D P    ITFTGS   G R+   +       +H
Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASV------EH 239

Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339
            ++   EMGGK+  VV +DAD+ +A ++   SAF   GQ+C+A SR +V E ++D+ +  
Sbjct: 240 NRKYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAA 299

Query: 340 VIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG--TGDDSKGY 396
           + E  +  V         ++GPV+DQ   ++   YI IGKQEG +L  GG     D+ G+
Sbjct: 300 MGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGF 359

Query: 397 FIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHI 456
           +++P +F +   + R+ +EEIFGPV A  +V D+DEAL VAN+T +GL+  + T + KH 
Sbjct: 360 YLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHA 419

Query: 457 ERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510
              K+    G +  N    G  V +H PFGG K S    +  G      +   KT
Sbjct: 420 THFKRNAEAGMVMVNLPTAG--VDFHVPFGGRKASSYGPREQGKYAAEFYTNVKT 472


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: 600
Number of extensions: 40
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: 515
Length of database: 477
Length adjustment: 34
Effective length of query: 481
Effective length of database: 443
Effective search space:   213083
Effective search space used:   213083
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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