GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Marinobacter guineae M3B

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_099618346.1 CLH62_RS11815 betaine-aldehyde dehydrogenase

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



>NCBI__GCF_002744735.1:WP_099618346.1
          Length = 489

 Score =  372 bits (956), Expect = e-107
 Identities = 202/476 (42%), Positives = 286/476 (60%), Gaps = 9/476 (1%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +F+ G+F+ +  G+TF  INPAT + +  V     +    A+++A+      W  MTA  
Sbjct: 10  NFVHGRFLANRTGETFPVINPATGQAIYEVEVADESVQQAAIESARAGF-AEWSAMTAIA 68

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  +L +   L+ ER +EL+ +E  DTGKP   + ++D+   A    FF+    +I  E 
Sbjct: 69  RSRILLRAVALLRERNDELAAVEVRDTGKPWQEAEAVDVVTGADTLEFFAGLAPSI--EG 126

Query: 133 TQMD-DVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191
            Q D      Y  R P+G+   I  WN PL +  WK APALA GN ++ KP+E TPM A 
Sbjct: 127 NQQDLGGDFYYTRREPLGICAGIGAWNYPLQISCWKSAPALACGNAMIFKPSEETPMGAV 186

Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251
            LAEI  +AGVP GV N+V G      G  LT HP++  +SFTGE  TGK +MA+AA TL
Sbjct: 187 KLAEIFVEAGVPAGVFNVVQGAA--EVGQWLTHHPEIAKVSFTGEVATGKKVMAAAASTL 244

Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311
           K ++ ELGGK+P +IF D++L+  I   M  +F  QGE+C  G+R++V    Y  F+E+ 
Sbjct: 245 KDVTMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFMERM 304

Query: 312 VAKT-KELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK--RPEGLEK 368
           + +T K +  GDP D  T  GALIS++H + V  YI   + EG T+  GG+   PE  + 
Sbjct: 305 LERTRKNIKPGDPMDTNTNFGALISEKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKG 364

Query: 369 GYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLR 428
           GYF+EPTI T  T D  +VKEEIFGPV++V+ F  E+EV+ + N+T  GL+A V+TND+R
Sbjct: 365 GYFVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFSNEDEVIARANNTDTGLAAGVFTNDIR 424

Query: 429 RAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
           RAHRV  QI+AGI W+N++       P GG K SGIGRE G  +   Y+++ ++ I
Sbjct: 425 RAHRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYI 480


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: 602
Number of extensions: 28
Number of successful extensions: 6
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: 489
Length adjustment: 34
Effective length of query: 452
Effective length of database: 455
Effective search space:   205660
Effective search space used:   205660
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.

Links

Downloads

Related tools

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