GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pseudomonas fluorescens FW300-N2E2

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Pf6N2E2_1381 Aldehyde dehydrogenase (EC 1.2.1.3)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1381
          Length = 506

 Score =  347 bits (891), Expect = e-100
 Identities = 194/480 (40%), Positives = 281/480 (58%), Gaps = 12/480 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +FI G+FV  ++G+ F N +P   E +       AA+ID A+ AA  A +  W K +  +
Sbjct: 21  NFIGGEFVAPVNGEYFTNTSPVNGEVIAEFPRSSAADIDKALDAAHAAADA-WGKTSVQD 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  RSLVLLKIADRIEQNLEILAVSETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGGA 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
             E+  D  +P GV+N+VHGFG   AG AL     +  I+FTG T  G  IM  AA+ + 
Sbjct: 200 FIELVADL-LPPGVLNIVHGFG-REAGEALATSKRIAKIAFTGSTPIGSHIMKCAAENII 257

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

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

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

Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
            D+ RA+R+   I+AG VW N + L      FGG K+SG+GRE      + Y +  N+ +
Sbjct: 437 RDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNLLV 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: 615
Number of extensions: 26
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