GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Phaeobacter inhibens BS107

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase

Query= reanno::Smeli:SM_b20891
         (477 letters)



>FitnessBrowser__Phaeo:GFF501
          Length = 476

 Score =  619 bits (1597), Expect = 0.0
 Identities = 310/475 (65%), Positives = 372/475 (78%), Gaps = 2/475 (0%)

Query: 4   HQNLIAGEWVGG-DGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILE 62
           ++NLIAG+W       ANINPS+T DV+G  A + AED + AIAAA+ A P W+ S   +
Sbjct: 3   YKNLIAGDWSETVAAAANINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQQ 62

Query: 63  RHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVV 122
           R  +L     EILARK ELG+LLSREEGKTL EGIGE  RAGQIF+FFAGETLR AGE++
Sbjct: 63  RFDVLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEIL 122

Query: 123 PSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWA 182
            SVRPG+GVE+TR P GVVG+ITPWNFPIAIPAWK+APAL YG+ +V KPAEL PGC+ A
Sbjct: 123 GSVRPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAHA 182

Query: 183 IVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRK 242
           + +I++R+GLP+GV N+V G GS VGQ ++ S  V AI+FTGS  TG  +A A     +K
Sbjct: 183 LAEIINRSGLPEGVFNIVFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQRKK 242

Query: 243 YQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGE 302
            QLEMGGKNP VVLDDADL  AV+A++N AFFSTGQRCTASSR+IVTEGIHDRFVAA+GE
Sbjct: 243 LQLEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDRFVAALGE 302

Query: 303 RIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQ 362
           R+ GL V +AL   T IGPVVD+ QL +D  Y+ +   EG ++  GG+ + R T GFYL 
Sbjct: 303 RMTGLRVGNALDDSTQIGPVVDERQLEKDLYYLDVAASEGGQV-LGGQTLQRSTKGFYLA 361

Query: 363 PALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHF 422
           PAL TE +N+MRI++EE+FGP+A+VIRV DYDEAL VANDTPFGLS+GI T SLK+ATHF
Sbjct: 362 PALVTETSNDMRINQEEVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATHF 421

Query: 423 KRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAYTLA 477
           K +AEAGM MVNLPTAGVD+HVPFGG K SS+G REQG +A EFYT VKTAYTLA
Sbjct: 422 KAHAEAGMAMVNLPTAGVDYHVPFGGTKGSSFGAREQGSHAKEFYTKVKTAYTLA 476


Lambda     K      H
   0.317    0.134    0.391 

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: 748
Number of extensions: 31
Number of successful extensions: 2
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: 477
Length of database: 476
Length adjustment: 33
Effective length of query: 444
Effective length of database: 443
Effective search space:   196692
Effective search space used:   196692
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: 51 (24.3 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