GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella amazonensis SB2B

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= metacyc::MONOMER-11537
         (425 letters)



>FitnessBrowser__SB2B:6937472
          Length = 405

 Score =  225 bits (573), Expect = 2e-63
 Identities = 146/407 (35%), Positives = 208/407 (51%), Gaps = 34/407 (8%)

Query: 25  PIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84
           PI       + + D +GREFIDFAGGIAV   GH HP +++A+TEQ  KL H     +  
Sbjct: 20  PIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSALTEQAQKLWHLS-NTMTN 78

Query: 85  EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAAT------GRAGVIAFTGA 138
           EP + L + +   V   FA+K     +G+EA E A+K+ R          ++ +IAF   
Sbjct: 79  EPALMLAKHL---VDNTFAEKVYFANSGAEANEAALKLVRRVALNKFGADKSQIIAFKQG 135

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEP 198
           +HGRT+ T+ + G+   YS G G  P  I  A Y N          + S++ +  +    
Sbjct: 136 FHGRTLFTVSVGGQPA-YSDGFGPKPADIDHAEYNN----------LDSLKALISDRT-- 182

Query: 199 RDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQM 258
               A+++EP+QGEGG      EF+K +R LCDQH  LL+ DEVQTG GRTG  +A   +
Sbjct: 183 ---CAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGL 239

Query: 259 GVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEE 318
           GVT D+ T AK++ GGFP+  +    E    +  G  G TY G+P+ACA  LA       
Sbjct: 240 GVTPDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNT 299

Query: 319 EHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAQVV 378
             +L+  K   +    GL AI  KY V  EVR  G ++   L  N D     A      +
Sbjct: 300 PEVLNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGAAL--NAD----YAGKARDFM 353

Query: 379 AKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425
             A ++G++LL  G   NV+R    L  P+A + +GLA  +   A+L
Sbjct: 354 LAAAEEGVLLLMAGQ--NVVRFAPSLIIPEADVREGLARFDAAIAKL 398


Lambda     K      H
   0.320    0.137    0.394 

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: 427
Number of extensions: 21
Number of successful extensions: 5
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: 425
Length of database: 405
Length adjustment: 31
Effective length of query: 394
Effective length of database: 374
Effective search space:   147356
Effective search space used:   147356
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: 50 (23.9 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