GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Shewanella sp. ANA-3

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 7023382 Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>lcl|FitnessBrowser__ANA3:7023382 Shewana3_0612 succinylglutamic
           semialdehyde dehydrogenase (RefSeq)
          Length = 487

 Score =  167 bits (423), Expect = 8e-46
 Identities = 149/468 (31%), Positives = 217/468 (46%), Gaps = 28/468 (5%)

Query: 9   HYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRR 68
           H+I G+ QA     +++  NPA   +  R   A    V+AAV +A  A   W       R
Sbjct: 3   HFIKGQWQAGKGHDVTSS-NPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDGR 61

Query: 69  SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLK-TDFS 127
            +++  ++  L+ +  ELA+ I++E GK   +   EV   I  +  +  A N    T+ +
Sbjct: 62  LKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSATAYNKRTGTEAN 121

Query: 128 DNIGGGIDNWNLR-QPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186
           D   G      LR +P GV A   P+NFP  +P   I  AL+AGN  + KPSE  P  + 
Sbjct: 122 DTPAGRAV---LRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAE 178

Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246
           LM  L  +AGLP GV N+VQG+     AL  HP ++ + F GS+     +HQQ      +
Sbjct: 179 LMVSLWEKAGLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGK 238

Query: 247 VQALG-GAKNHMIVMPDADLDQAADALIGAAYGSAGERC-MAISIAVAVGDVGDELIAKL 304
           + AL  G  N +I+   AD+  A   ++ +AY S+G+RC  A  + V  G+ GD L+AKL
Sbjct: 239 ILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKL 298

Query: 305 LPRIDQLKIGN-GQQPGTDMGPLVT-AEHKAKVEGFIDAGVAEGARLI-----VDGRGFK 357
           +  + Q+K+G    QP   MG +++ A  K  V    +     G  L+       G G  
Sbjct: 299 VEAVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLQNLGGVSLVELSHLQAGTGLV 358

Query: 358 VPGAEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSC 417
            PG          L D VTA   +  +E FGP+L +VR  DF  A+ L N   +G     
Sbjct: 359 SPG----------LID-VTAVGELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGI 407

Query: 418 FTRDGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHA 465
                     F   I+ G+V  N  I        FGG   S  G+H A
Sbjct: 408 LADSRDDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGAS--GNHRA 453


Lambda     K      H
   0.320    0.137    0.412 

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: 516
Number of extensions: 21
Number of successful extensions: 3
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: 500
Length of database: 487
Length adjustment: 34
Effective length of query: 466
Effective length of database: 453
Effective search space:   211098
Effective search space used:   211098
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 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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