GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pedobacter sp. GW460-11-11-14-LB5

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__Pedo557:CA265_RS24850
          Length = 454

 Score =  224 bits (571), Expect = 5e-63
 Identities = 145/437 (33%), Positives = 220/437 (50%), Gaps = 9/437 (2%)

Query: 31  INPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEE 90
           INPAT E + ++ E   + + L   A +KA    W   T  ERIAV+    DL+    E+
Sbjct: 4   INPATAEIITSLEEDNLSTLQLKFDALQKA-QPQWAGKTLQERIAVITHFSDLLEVEIEK 62

Query: 91  LSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIR-RPVG 149
           L+ + + + GKP   S + +I  A     +          +    D+  +   I+  P+G
Sbjct: 63  LASVLTSEVGKPLQQSRN-EINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPLG 121

Query: 150 VIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNL 209
           V+  I+ WN P L+      PAL +GNTV+ KP+E   +T   + ++ + AGVPD V ++
Sbjct: 122 VVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFHI 181

Query: 210 VHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIFAD 269
               G    G+AL  + D N   FTG   TGK+I    A  +     ELGGK+P  I  D
Sbjct: 182 A--IGAKETGSALL-NMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDD 238

Query: 270 -SNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAKT 328
            +++      T   +F N G+ C    RIYV+   Y+ +   FV + K    G P     
Sbjct: 239 VTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEGV 298

Query: 329 KVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVVK 388
            +GAL   E    +   +K A+ +G  +LTGGK  EG  KGY+ EPT++T +T D  V++
Sbjct: 299 YIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEG--KGYYFEPTVLTDVTNDMLVMQ 356

Query: 389 EEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVNTWF 448
           EE FGP++ ++    + E L+ + DT YGL+ASV+T    RA ++  Q++AG  + N   
Sbjct: 357 EESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCD 416

Query: 449 LRDLRTPFGGMKQSGIG 465
                 P+ G K SGIG
Sbjct: 417 RVSAALPWSGRKYSGIG 433


Lambda     K      H
   0.318    0.136    0.404 

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: 511
Number of extensions: 27
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: 486
Length of database: 454
Length adjustment: 33
Effective length of query: 453
Effective length of database: 421
Effective search space:   190713
Effective search space used:   190713
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 (21.7 bits)
S2: 51 (24.3 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