GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Dietzia timorensis ID05-A0528

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_067474647.1 BJL86_RS10335 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_001659785.1:WP_067474647.1
          Length = 494

 Score =  232 bits (592), Expect = 2e-65
 Identities = 159/457 (34%), Positives = 234/457 (51%), Gaps = 31/457 (6%)

Query: 55  INPADKEEVVGRVSKASQEHAEQAIQAAAKAFEE--WRYTSPEERAAVLFRAAAKVRRRK 112
           I PAD  +V G VS+AS    E AI AA +AF+   W      ER   L   A ++RRRK
Sbjct: 26  ICPADGTDV-GVVSEASTADTESAIAAARRAFDSRVWADRPAGERGDFLLDVAEQLRRRK 84

Query: 113 HEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEK-NQYVYTP 171
            EF+     + GK   EA+ D  + I    ++ + + +   G+ V++ +    ++ VY P
Sbjct: 85  DEFARAEALDTGKRLVEAEGDMDDIIACFRFFGK-IADHDPGRLVDAGDNSVISRVVYEP 143

Query: 172 TGVTVVIPPWNFLFAIMAGTTVAP-IVTGNTVVLKPASATPVIAAKFVEVLEESGLPKGV 230
            GV  +I PWNF   + A   +AP +  GN+ V+KPA  TP      ++V+++ GLP GV
Sbjct: 144 IGVCGMITPWNFPL-LQASWKIAPALAAGNSFVIKPAELTPHTTILILDVIDKLGLPAGV 202

Query: 231 VNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQHLKRVIAEMGGK 290
            N V G G  VG  L  HP   L++FTG    G +I E AA   PG   +K+V  E+GGK
Sbjct: 203 ANLVLGDGGTVGAPLSSHPDIDLVSFTGGLVTGRKIAEAAA---PG---IKKVALELGGK 256

Query: 291 DTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITESKVTA 350
           +  VV  DAD + A  +   + F  +G  CSAG+R +V + + ++ ++ ++   E  V  
Sbjct: 257 NPNVVFADADFDAAVDNALNAGFVDSGLVCSAGTRLIVQDTIAEKFVDALVRRAEGIVMG 316

Query: 351 KPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSG---GTGDDSKGYFIKPTIFADL 406
            P   +   GP+I +   DK+  Y++ G   G RL +G   G  +  KGYF  PTI    
Sbjct: 317 GPLDENAETGPLISEAHRDKVTDYVKRGVDAGARLRTGGHWGGPEHEKGYFYAPTILDQC 376

Query: 407 DPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIERAKQEFHVG 466
                 + EE FGPV+     S  +EA+E+AN+TEYGL GAV +++     R  +    G
Sbjct: 377 TKDNPAVIEEGFGPVITVETFSTEEEAVEIANHTEYGLAGAVWSSDAGTANRVSRRLRHG 436

Query: 467 NLYFNRNCTGAIVGYHPF------GGFKMSGTDSKAG 497
            ++ N         YHP+      GGFKMSG   + G
Sbjct: 437 TIWIN--------DYHPYVPQAEWGGFKMSGVGRELG 465


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: 647
Number of extensions: 41
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: 494
Length adjustment: 34
Effective length of query: 481
Effective length of database: 460
Effective search space:   221260
Effective search space used:   221260
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