GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS09465 HSERO_RS09465 aldehyde
           dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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