GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Dyella japonica UNC79MFTsu3.2

Align 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

Query= SwissProt::P23105
         (486 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4232
          Length = 1074

 Score =  160 bits (405), Expect = 2e-43
 Identities = 143/471 (30%), Positives = 214/471 (45%), Gaps = 25/471 (5%)

Query: 15   SASGKLFDNVSPANG-QVIGRVHEAGRAEVDAAVRAARAALKGPWGKMTVAERAEILHRV 73
            +++G      +PA+  QV+G    A  A V+ A+  A AA  G W ++  A RA IL   
Sbjct: 590  TSAGATVQVTNPADRRQVVGSYVSADSATVEKALANAVAAQHG-WDRLPAASRAAILEHA 648

Query: 74   ADGITARFGEFLEARMPGHRQAEVAGQPHRHSARR--ANF-KVFADLLKNVANEAFEMAT 130
            A+ + AR GEF+   +   R+A   G P   +  R  A+F + +A + +    +  ++  
Sbjct: 649  AEQLEARRGEFIALCV---REAG-KGLPDAIAEIREAADFLRYYATMARRYFGQPEQLPG 704

Query: 131  PDGAGALNYGVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNCVVVKPSEETPLTATLL 190
            P G    N      +GV   ISPWN PL +   +V  ALA GN V+ KP+E+T L     
Sbjct: 705  PTGES--NQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAA 762

Query: 191  GEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGETIMRAAA---KG 247
             +++  AGVPA V   + G  G + GA LT  P V    FTG T T   I RA A     
Sbjct: 763  VQLLHEAGVPADVLQYLPG-DGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAP 821

Query: 248  VRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDAFVAR 307
            +  +  E GG+NA I  +    ++ ++  + SAF + GQ C     +YV+  I D   A 
Sbjct: 822  IAALIAETGGQNAMIADSSALPEQIVKDAVSSAFQSAGQRCSAARVLYVQEDIADKVCAM 881

Query: 308  LKAGAEALKIGEPNDPEANFGPLISHKPREKVPSYYQQAVDDGATVVTGGGVPEMPAHLA 367
            L      LK+G+P     + GP+I    R K+   +   +D  A  +  G V   PA   
Sbjct: 882  LAGAMAELKVGDPAQLSTDVGPVIDEDAR-KILVDHAARMDQEAKKI--GEVALDPATTG 938

Query: 368  GGAWVQPTIWTGLADDSAVVTEEIFGPCCHIRPFDSEE--EAIELANSLPYGLASAIWTE 425
             G +  P  +       A +T EIFGP  H+  +   E  + ++  N+  YGL   I + 
Sbjct: 939  NGTFFAPRAYE--IPGLATLTREIFGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSR 996

Query: 426  NVRRAHRVAGQIEAGIVWVNSWFLRDL--RTAFGGSKQSGIG-REGGVHSL 473
                   +  +   G  +VN   +  +     FGG   SG G + GG H L
Sbjct: 997  IDDTVEFIQSRARVGNCYVNRNQIGAVVGVQPFGGEGLSGTGPKAGGPHYL 1047


Lambda     K      H
   0.318    0.136    0.413 

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: 1087
Number of extensions: 67
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: 486
Length of database: 1074
Length adjustment: 40
Effective length of query: 446
Effective length of database: 1034
Effective search space:   461164
Effective search space used:   461164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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