GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Klebsiella michiganensis M5al

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate BWI76_RS03865 BWI76_RS03865 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

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



>FitnessBrowser__Koxy:BWI76_RS03865
          Length = 488

 Score =  429 bits (1102), Expect = e-124
 Identities = 219/479 (45%), Positives = 315/479 (65%), Gaps = 11/479 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           H+I+GK V   D   F   NPAT E L  VA GGA E++ AV AAK+A    W  +   E
Sbjct: 6   HWINGKNVAGSD--YFHTTNPATGEVLAEVASGGADEVNQAVAAAKEAFP-KWANLPMKE 62

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  ++R++GDLI +   E++ +E+ DTG P   + ++ IPRA++NF FF++  + +  + 
Sbjct: 63  RARLMRRLGDLIDQNVPEIAAMETADTGLPIHQTKNVLIPRASHNFEFFAEVCQQMNGKT 122

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
             +DD  LNY + +PVGV  L++PWN+P +  TWK+AP LA GNT V+K +EL+P+TA  
Sbjct: 123 YPVDDKMLNYTLVQPVGVCALVSPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTADR 182

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           L E+  +AG+P GV+N+V G+G  +AG AL  H DV A+SFTG T TG+ IM +A   LK
Sbjct: 183 LGELALEAGIPAGVLNVVQGYGA-TAGDALVRHHDVRAVSFTGGTATGRNIMKNAG--LK 239

Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312
           + S ELGGK+P +IF D++++  ++  + + F   GE C  GSRI++++  Y  F+++F 
Sbjct: 240 KYSMELGGKSPVLIFEDADIERALDAALFTIFSINGERCTAGSRIFIQQSIYPEFVKRFA 299

Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG-----KRPEGLE 367
            +   L VGDP D  T+VGALIS +H+E+V+GYI+L +EEG T+L GG       P  L 
Sbjct: 300 ERANRLRVGDPTDPNTQVGALISQQHWEKVSGYIRLGIEEGATLLAGGADKPTDLPAHLR 359

Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427
            G FL PT++  +    RV +EEIFGPV  ++PF  E E L   ND  YGL++ +WT D+
Sbjct: 360 NGNFLRPTVLADVDNRMRVAQEEIFGPVACLLPFKDEAEGLRLANDVEYGLASYIWTQDV 419

Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
            +  R+A  IEAG+V+VNT  +RDLR PFGG+K SG GREGG +SFE ++E+ N+CI +
Sbjct: 420 SKVLRLARGIEAGMVFVNTQNVRDLRQPFGGVKASGTGREGGEYSFEVFAEMKNVCISM 478


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: 612
Number of extensions: 26
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: 488
Length adjustment: 34
Effective length of query: 452
Effective length of database: 454
Effective search space:   205208
Effective search space used:   205208
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