GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Algiphilus aromaticivorans DG1253

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_043765410.1 U743_RS02990 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_000733765.1:WP_043765410.1
          Length = 508

 Score =  245 bits (626), Expect = 2e-69
 Identities = 163/480 (33%), Positives = 241/480 (50%), Gaps = 34/480 (7%)

Query: 27  ATVSEYLGKDYPLVINGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAK 84
           A  ++Y  K+Y   I+G+ V+  +  +I  INPA+ + V+  +   + E A +A+ AAA+
Sbjct: 14  AQAAKYFQKEYGHFIDGKWVQGASGERIPMINPANGQ-VLSHIQSGNAEDARRAVDAAAQ 72

Query: 85  AFEEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEY 143
           AF  W  T   ER  VL+  A ++R R  +++ +   + GKP  EA   D   AI+  E 
Sbjct: 73  AFPAWSQTPRSERQRVLYEMARRLRARMADYAMMDCLDNGKPAMEAMHFDLPMAIEQFEI 132

Query: 144 YAR-------QMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPI 196
           ++        Q I+      +  RE         P GV   I PWN    +MA      +
Sbjct: 133 FSGAPWFLHGQSIDAPNTLGIVLRE---------PLGVVAQIIPWNVPLIMMAAKLAPAL 183

Query: 197 VTGNTVVLKPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITF 256
             GNTVVLKP+    +   +F   + +  LP GVVN V G G  VG+ LV HPK   + F
Sbjct: 184 AAGNTVVLKPSEIVCLSVLEFFREMADL-LPPGVVNVVTGYGPSVGEALVTHPKVRKVAF 242

Query: 257 TGSREVGTRIFERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFA 316
           TGSR    ++ + A+       ++     E+GGK   +V EDAD++ AA+    S     
Sbjct: 243 TGSRPTAQKLMQYASV------NIIPQTMELGGKSANIVCEDADLDAAAEGAAMSTVLNK 296

Query: 317 GQKCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIE 376
           G+ C AGSR  VHEKV D  L++   + +      P      +GP + +  YDKIM Y+E
Sbjct: 297 GEVCLAGSRVFVHEKVKDVFLDKFTSLLKRVKAGDPREPTTQIGPQVSKAQYDKIMGYLE 356

Query: 377 IGKQEG-RLVSGGTGDDSKGY----FIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFD 431
           +G+QEG +L +GG      G+    FI+PT+F D+D   R+ QEEIFGPV       D D
Sbjct: 357 LGQQEGAKLAAGGRKAAPAGFEDGLFIEPTVFFDVDNSMRIAQEEIFGPVSCVIGFRDDD 416

Query: 432 EALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491
           E + +AN++ YGL G + T +     R  +    G ++ NR      +G  P GG+K SG
Sbjct: 417 EVVRMANDSVYGLGGGLWTKDLSRAHRIARALETGTVWVNRYYN--FLGGMPIGGYKQSG 474


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: 602
Number of extensions: 30
Number of successful extensions: 5
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 Sep 24 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