GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kauB in Escherichia coli BW25113

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Keio:14450
          Length = 490

 Score =  357 bits (915), Expect = e-103
 Identities = 189/482 (39%), Positives = 286/482 (59%), Gaps = 7/482 (1%)

Query: 19  EGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQL 78
           E + +I+G YT A SG TFE ++P +G  LA V +    D +RAV++A+      +W+ +
Sbjct: 6   EQQLYIHGGYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQ--GQKIWASM 63

Query: 79  APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138
              +R   L R  D+LR+  +ELA LETLD GK   ++S++DI   A  + + A  I  +
Sbjct: 64  TAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIPAL 123

Query: 139 YDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198
                P          REP+GVV  I  WN+P+ +A WK  PALA GN+++ KPSE +PL
Sbjct: 124 EGSQIPLRETSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPL 183

Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258
           TA+++A++  EAG+P GV NVLPG G   G+ L  H  +  + FTG     K++M  +  
Sbjct: 184 TALKLAEIYSEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMANSAA 243

Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
           S++K + +E GGKSP IVF DA DL  AA+ A  A  F+ G+VCT G+R+ V    K  F
Sbjct: 244 SSLKEVTMELGGKSPLIVFDDA-DLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKAAF 302

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378
              ++  ++  + G+  DPQT  G LV     + VL YI  G ++GA++L GG   L+  
Sbjct: 303 EQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGGD-VLKGD 361

Query: 379 G---GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435
           G   G +V PT+F   ++ M I +EEIFGPV+S++ +++ +E +  ANDT YGLAAGI T
Sbjct: 362 GFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGIVT 421

Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWI 495
           +D+++AH+    + AG  W+N +       P GG+K SG GR+  +  L+ YT++K+  +
Sbjct: 422 ADLNRAHRVIHQLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVMTLQSYTQVKSIQV 481

Query: 496 KL 497
           ++
Sbjct: 482 EM 483


Lambda     K      H
   0.316    0.132    0.390 

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: 627
Number of extensions: 34
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: 497
Length of database: 490
Length adjustment: 34
Effective length of query: 463
Effective length of database: 456
Effective search space:   211128
Effective search space used:   211128
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 (21.6 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