GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Herbaspirillum seropedicae SmR1

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS09465
          Length = 506

 Score =  361 bits (927), Expect = e-104
 Identities = 200/480 (41%), Positives = 278/480 (57%), Gaps = 12/480 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +FI GKFVP + G+ F+NI+P        VA   A +++LA+ AA  A    W K +  E
Sbjct: 21  NFIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKKS-WGKTSPTE 79

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  +L K+ D +    E L+  E+LD GKP   + + DIP A  +F +F+  +RT     
Sbjct: 80  RANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVRTQEGSI 139

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
             +D+    Y    P+GV+G I PWN P+L+  WKLAPALAAGN VV+KPAE TP +  V
Sbjct: 140 CPIDNDTYAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASIMV 199

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           L E+  D  +P GVVN+V GFG   AG  L  +  +  I+FTGETTTG++IM  A++ L 
Sbjct: 200 LIELIADL-IPPGVVNIVQGFGV-EAGKPLASNKRIAKIAFTGETTTGRLIMQYASQNLI 257

Query: 253 RLSYELGGKNPNVIFAD--SNLDEVIETTMKS---SFINQGEVCLCGSRIYVERPAYEAF 307
            ++ ELGGK+PN+ FAD     D+  +  ++      +NQGEVC C SR+ V+   YE F
Sbjct: 258 PVTLELGGKSPNIFFADVLDKDDDFFDKALEGFAMFALNQGEVCTCPSRVLVQESIYERF 317

Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE--- 364
           +E+ + +   +  G+P D  T +GA  S E  E++  YI +  +EG  +L GG R E   
Sbjct: 318 IERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGGGREELGG 377

Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424
            L  GY+++PT+  G     R+ +EEIFGPVV+V  F  EEE L   NDT YGL A +WT
Sbjct: 378 DLASGYYVKPTVFQG-NNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGLGAGLWT 436

Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
            D  RA R+  +I+AG VW N + L      FGG KQSGIGRE      + Y +  N+ +
Sbjct: 437 RDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLV 496


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: 591
Number of extensions: 35
Number of successful extensions: 7
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: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
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: 52 (24.6 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