GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Pseudomonas fluorescens GW456-L13

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate PfGW456L13_3517 Aldehyde dehydrogenase (EC 1.2.1.3)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3517 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 506

 Score =  351 bits (900), Expect = e-101
 Identities = 197/480 (41%), Positives = 282/480 (58%), Gaps = 12/480 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +FI G+FV  ++G+ F N +P   E +       AA+ID A+ AA  A +  W K +A +
Sbjct: 21  NFIGGEFVAPINGEYFTNTSPVNGEVIAEFPRSSAADIDKALDAAHAAADA-WGKTSAQD 79

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  VL K+ D I +  E L+V E+ D GK    + + D+P AA +F +F+  IR     A
Sbjct: 80  RSLVLLKIADRIEQNLEVLAVTETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGGA 139

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
            +++++   Y    P+GV+G I PWN PLL+  WKLAPALAAGN +V+KPAE TP++  V
Sbjct: 140 AEINELTTAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPLSIMV 199

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
            AE+  D  +P GV+N+V GFG   AG AL     +  I+FTG T  G  IM  AA+ + 
Sbjct: 200 FAELIADL-LPAGVLNIVQGFG-REAGEALATSKRIAKIAFTGSTPVGAHIMHCAAENII 257

Query: 253 RLSYELGGKNPNVIFADSNLDE--VIETTMKS---SFINQGEVCLCGSRIYVERPAYEAF 307
             + ELGGK+PN+ F D    E   IE   +    +F NQGEVC C SR  V+   YE F
Sbjct: 258 PSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEVCTCPSRALVQESIYEPF 317

Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG--KRPEG 365
           + + + K  ++  G+P D +T VGA  S++ Y+++  Y+ +A EEG  +LTGG  +R EG
Sbjct: 318 MAEVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLTIAQEEGAELLTGGAAERLEG 377

Query: 366 -LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424
            L  GY+++PT++ G  +  RV +EEIFGPVV V  F  E E L   ND+ +GL A +WT
Sbjct: 378 DLSSGYYIQPTLLKGHNK-MRVFQEEIFGPVVGVTTFKDEAEALAIANDSEFGLGAGLWT 436

Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
            D+ RA+R+   I+AG VW N + L      FGG K+SG+GRE      + Y +  N+ +
Sbjct: 437 RDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKMMLDHYQQTKNLLV 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: 608
Number of extensions: 28
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.

Links

Downloads

Related tools

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