GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SM_b20891
          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 (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