GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Phaeobacter inhibens BS107

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC

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



>FitnessBrowser__Phaeo:GFF3171
          Length = 503

 Score =  386 bits (991), Expect = e-111
 Identities = 201/455 (44%), Positives = 284/455 (62%), Gaps = 5/455 (1%)

Query: 28  FDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILER 87
           F  I+P  +  +  VA G AA+ID A QAA++A    W+ + A +R  +L ++ + I  R
Sbjct: 39  FQTISPVDKSVICDVAHGTAADIDAAAQAARQAF-AEWRDLPAVQRKKILIRIAEGIEAR 97

Query: 88  KEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIRRP 147
            EE+++ E  DTG+         + R A NF +F+D +    +         +N   R P
Sbjct: 98  AEEIALCECWDTGQAYKFMSKAAL-RGAENFRYFADQVVQARDGQHLQSPTLMNVTTRVP 156

Query: 148 VGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVV 207
           +G +G+I PWN P +L TWK+APALAAG TVV KPAE +P+TA +L EI  +AG+P GV+
Sbjct: 157 IGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTARLLVEIAEEAGLPPGVL 216

Query: 208 NLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIF 267
           N V+GFG + AG AL EHP + AI+F GE+ TG +I    A TLKR   ELGGKNP ++F
Sbjct: 217 NTVNGFG-DEAGKALCEHPAIRAIAFVGESRTGSLITKQGADTLKRNHLELGGKNPVIVF 275

Query: 268 ADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAK 327
            D++L+  ++  +   +   GE C   SR+ ++    + F  + + +   + VG P D  
Sbjct: 276 EDADLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARLIERINNIKVGHPLDPT 335

Query: 328 TKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVV 387
           T++G L+S+EH+ +VT Y  +A +EG TI  GG+ P G E+GYF+ PT+ T    D R+ 
Sbjct: 336 TEIGPLVSEEHFNKVTSYFDIATKEGATIAAGGE-PVG-EEGYFIRPTLFTDARNDMRIA 393

Query: 388 KEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVNTW 447
           +EEIFGPV+T IPF TE E L   NDT YGL+  +WTNDL RA R   ++EAG++WVN+ 
Sbjct: 394 QEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTNDLTRALRFTDRLEAGMIWVNSE 453

Query: 448 FLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482
            +R L TPFGG+K SGIGR+GG  SFEFY E  +I
Sbjct: 454 NVRHLPTPFGGVKASGIGRDGGDWSFEFYMEQKHI 488


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: 631
Number of extensions: 31
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: 503
Length adjustment: 34
Effective length of query: 452
Effective length of database: 469
Effective search space:   211988
Effective search space used:   211988
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