GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Tistlia consotensis USBA 355

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_900177295.1:WP_179243903.1
          Length = 480

 Score =  285 bits (728), Expect = 3e-81
 Identities = 173/483 (35%), Positives = 264/483 (54%), Gaps = 18/483 (3%)

Query: 40  VINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99
           +I GE V+      + NP+D  +VVG  ++     A QAI AAA AF  W  ++P++R  
Sbjct: 7   LIAGEWVDAPNASENRNPSDLSDVVGLYAQGDAAQAGQAIDAAAAAFPAWSRSTPQQRFD 66

Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159
           +L  A  ++  RK E   LL +E GK   E   +T  A    +++A + + +A  +  ++
Sbjct: 67  ILDAAGTEILARKEELGRLLSREEGKTLPEGIGETVRAGQIFKFFAGEALRIAGDRIDST 126

Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219
           R G   +    P GV  +I PWNF  AI A      +  GN VV+KPA   P  A    +
Sbjct: 127 RPGVIAEATREPLGVVGLITPWNFPIAIPAWKLAPALAFGNCVVMKPADLVPGCAWALAD 186

Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279
           +L+ +GLPKGV N V G G+ VG+ ++  PK + I+FTGS   G  +  R  +     + 
Sbjct: 187 ILQRAGLPKGVFNLVMGRGSVVGEAILASPKVAAISFTGSVATGRHVARRCIE----GEA 242

Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339
           +K+   EMGGK+  VV +DAD+E+AA S    AF   GQ+C+A SR +V E ++D    R
Sbjct: 243 MKKFQLEMGGKNPFVVLDDADLEVAANSALNGAFFSTGQRCTASSRLIVTEGIHD----R 298

Query: 340 VIEITESKVTA-KPDSA---DVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG--TGDD 392
            +E   SK+ A K D+A      +GPV+DQ   D+ + YI++G+ EG +L  GG     +
Sbjct: 299 FVEALTSKLKALKVDNALKEGTQIGPVVDQRQLDQDLDYIKVGQDEGAKLAWGGERLNRE 358

Query: 393 SKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNN 452
           ++G++++P +F + D   R+ +EEIFGPV +  +V D+D AL VAN+T++GL+  + T++
Sbjct: 359 TEGFYLQPALFTETDNAMRINREEIFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSS 418

Query: 453 RKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKTI 511
            KH E  K+    G +  N    G  V YH PFGG K S   ++  G   +  +   KT 
Sbjct: 419 LKHAEHFKRNSQAGMVMVNLPTAG--VDYHVPFGGRKNSSYGAREQGRYAVEFYTTVKTA 476

Query: 512 SEM 514
             M
Sbjct: 477 YAM 479


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: 568
Number of extensions: 27
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: 480
Length adjustment: 34
Effective length of query: 481
Effective length of database: 446
Effective search space:   214526
Effective search space used:   214526
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 Apr 09 2024. 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