GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Streptacidiphilus oryzae TH49

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_037568600.1 BS73_RS01225 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

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



>NCBI__GCF_000744815.1:WP_037568600.1
          Length = 501

 Score =  307 bits (787), Expect = 5e-88
 Identities = 179/470 (38%), Positives = 255/470 (54%), Gaps = 11/470 (2%)

Query: 12  WVGGDGVANINPS--NTDDVVGE--YA---RASAEDAKAAIAAAKAAFPAWSRSGILERH 64
           W+GG    +++ +     + VG   YA   R SA D  AA+ AAKAAFPAWS  G   R 
Sbjct: 18  WIGGRPAPSLDGAVFEVSEPVGNTPYATASRGSAADVDAAVQAAKAAFPAWSALGDRARA 77

Query: 65  AILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPS 124
             L + AD + AR + L    + + G  + +  G+  RA + F +FA   + L GE    
Sbjct: 78  TALNRIADAVEARHERLSAFETFDTGLPVTQSRGQARRAAENFRYFADVLVALGGEAFRQ 137

Query: 125 VRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIV 184
               I   + R PAGV G+ITPWN P  + +WKLAPAL  G T+V KPAE  P  +    
Sbjct: 138 GSSQISYTV-RRPAGVAGLITPWNTPFMLESWKLAPALAAGCTLVLKPAEWTPLSASLWP 196

Query: 185 DILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQ 244
           +I   AGLP G +N+V G G   GQA++D P+V  I+FTGSTATG+ +  +S EH +   
Sbjct: 197 EIFAEAGLPDGTVNIVHGIGEEAGQALVDHPEVPRISFTGSTATGRHIVRSSAEHLKTLS 256

Query: 245 LEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERI 304
           +E+GGK+P VV  DADL  A+++ V   F   G+RCTA SR++V   +++ F A + ER 
Sbjct: 257 MELGGKSPAVVFADADLDAALDSVVFGVFSLNGERCTAGSRVLVERPVYEEFTARLAERA 316

Query: 305 KGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQPA 364
             + V     P T +G +V      +   Y+ +G++E   LA GG        G YLQP 
Sbjct: 317 SRVRVGPPQDPATEVGALVHPEHYARVQGYLELGRKEARLLAGGGRP-EHLPEGNYLQPT 375

Query: 365 LFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKR 424
           +F +   + RI +EEIFGPV         +EA+ +AN TP+GL++ + T+ L        
Sbjct: 376 VFADVPRDARIFQEEIFGPVVCAAPFDTEEEAVELANATPYGLAAYVWTSDLARGHRIAH 435

Query: 425 NAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAY 474
             E+GM+ +N      D   PFGG KAS  G RE G ++ +FY+  K  +
Sbjct: 436 AVESGMLWINSHNVR-DLRTPFGGVKASGLG-REGGAHSIDFYSETKIVH 483


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: 577
Number of extensions: 23
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: 477
Length of database: 501
Length adjustment: 34
Effective length of query: 443
Effective length of database: 467
Effective search space:   206881
Effective search space used:   206881
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 24 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