GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7023382
          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 (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