GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Klebsiella michiganensis M5al

Align succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate BWI76_RS03865 BWI76_RS03865 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_11505
         (480 letters)



>FitnessBrowser__Koxy:BWI76_RS03865
          Length = 488

 Score =  345 bits (884), Expect = 3e-99
 Identities = 191/476 (40%), Positives = 278/476 (58%), Gaps = 18/476 (3%)

Query: 19  WVDADN---GQTINVTNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERANK 75
           W++  N       + TNPATGE+L  V   GA E  +A+ AA +A P W  L  KERA  
Sbjct: 7   WINGKNVAGSDYFHTTNPATGEVLAEVASGGADEVNQAVAAAKEAFPKWANLPMKERARL 66

Query: 76  LRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASF-IEWFAEEAKRIYGDVIPGH 134
           +RR  +LI +N  ++A + T + G P+ + K  ++  AS   E+FAE  +++ G   P  
Sbjct: 67  MRRLGDLIDQNVPEIAAMETADTGLPIHQTKNVLIPRASHNFEFFAEVCQQMNGKTYP-- 124

Query: 135 QPDKRL-IVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSAFALA 193
             DK L   + QP+GV A ++PWN P    T K  P LA G T VLK +  +P +A  L 
Sbjct: 125 VDDKMLNYTLVQPVGVCALVSPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTADRLG 184

Query: 194 ELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKVS 253
           ELA  AGIP GVL+VV G     G  L  +  VR +SFTG T  GR +M      +KK S
Sbjct: 185 ELALEAGIPAGVLNVVQGYGATAGDALVRHHDVRAVSFTGGTATGRNIMKNAG--LKKYS 242

Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKVAV 313
           +ELGG +P ++F+DAD+++A++ A+ + +  NG+ C   +R++IQ S+Y  F ++     
Sbjct: 243 MELGGKSPVLIFEDADIERALDAALFTIFSINGERCTAGSRIFIQQSIYPEFVKRFAERA 302

Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGK---------VMEGN 364
            +L++G+  +  T  G LI  +   KV  +I   + +GATLLAGG          +  GN
Sbjct: 303 NRLRVGDPTDPNTQVGALISQQHWEKVSGYIRLGIEEGATLLAGGADKPTDLPAHLRNGN 362

Query: 365 FFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRV 424
           F  PT+L +V     VA+EE FGP+A L  FKDEAE + ++ND E+GLASY + +D+ +V
Sbjct: 363 FLRPTVLADVDNRMRVAQEEIFGPVACLLPFKDEAEGLRLANDVEYGLASYIWTQDVSKV 422

Query: 425 FRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480
            R+A  +E GMV VNT  + +   PFGG+KASG GREG +Y  E + E+K +C+ +
Sbjct: 423 LRLARGIEAGMVFVNTQNVRDLRQPFGGVKASGTGREGGEYSFEVFAEMKNVCISM 478


Lambda     K      H
   0.317    0.135    0.389 

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: 568
Number of extensions: 22
Number of successful extensions: 4
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: 480
Length of database: 488
Length adjustment: 34
Effective length of query: 446
Effective length of database: 454
Effective search space:   202484
Effective search space used:   202484
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