GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4232 N515DRAFT_4232 L-proline
            dehydrogenase /delta-1-pyrroline-5-carboxylate
            dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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