GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudarthrobacter sulfonivorans Ar51

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_001484605.1:WP_058929223.1
          Length = 508

 Score =  265 bits (678), Expect = 2e-75
 Identities = 164/488 (33%), Positives = 253/488 (51%), Gaps = 24/488 (4%)

Query: 35  KDYPLVINGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEE--WR 90
           + Y ++I+G  V++ +      ++P D     GRV  A+ E  ++A++AA +AF+E  W 
Sbjct: 19  RSYSMLIDGAWVQSSSGETFACVDPYDNASW-GRVPAATVEDVDRAVRAARRAFDEGGWP 77

Query: 91  YTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIE 150
            T P +RAA+L R A  +     E +   + E GK   E      +      Y A  + E
Sbjct: 78  QTLPSQRAALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMGQHAHYVAG-LAE 136

Query: 151 LAKGKPVNSREGEKNQYVYT-PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASA 209
             +G+ + S       + +  P GV  +I PWN    +++    A +  GNTVV+KP+ A
Sbjct: 137 TIQGRTIESNWPNTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEA 196

Query: 210 TPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFER 269
           TP    +  E+  E+G P GV+N V G G   G  LVDH     I FTGS   G  I ++
Sbjct: 197 TPTSTLRMAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQ 256

Query: 270 AAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVH 329
           AA      +   RV  E+GGK   ++  DADI+ A        FG  GQ C  GSR +V 
Sbjct: 257 AA------ERFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQ 310

Query: 330 EKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG 388
           + +YD  ++R+   T++     P    V MGPV ++  + K++ Y+++G+ EG  +V+GG
Sbjct: 311 DSIYDDFVDRMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGG 370

Query: 389 -----TGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYG 443
                T + SKG F +PT+FA++  ++RL QEEIFGPV +  +  D DEA+++AN +++G
Sbjct: 371 ARCMTTSELSKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFG 430

Query: 444 LTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYL 502
           L   V TN+     R  +    G ++ N   T  +  Y  PFGGFK SG   +  GPD L
Sbjct: 431 LAAGVWTNDVSRAHRMIRRVRSGTVWVN---TYRLTNYSVPFGGFKQSGIGREL-GPDAL 486

Query: 503 ALHMQAKT 510
             + + K+
Sbjct: 487 DAYTEVKS 494


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: 565
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: 508
Length adjustment: 35
Effective length of query: 480
Effective length of database: 473
Effective search space:   227040
Effective search space used:   227040
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