GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Phaeobacter inhibens BS107

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__Phaeo:GFF2829
          Length = 440

 Score =  197 bits (500), Expect = 7e-55
 Identities = 152/428 (35%), Positives = 216/428 (50%), Gaps = 57/428 (13%)

Query: 26  VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGK--FWHTGNGYTNEPV 83
           V G+G  L D  GK Y+D +GG AV+ LGH+   ++ A+ EQ GK  F HTG   T+EP 
Sbjct: 17  VAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGF-LTSEPA 75

Query: 84  LRLAKQLIDATFAD--RVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGR 141
             LA  LI     D  RV+F + G+EA EAA+KLAR+Y  +R  + +  ++A + ++HG 
Sbjct: 76  EALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGN 135

Query: 142 TLFTVSAGGQPAYSQDFAPLPPQIQHA---------------------IYNDLDSAKALI 180
           TL  ++AGG     Q FAPL   I H                      + N+L++    +
Sbjct: 136 TLGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRL 195

Query: 181 DDNTC-AVIVEPMQGE-GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAY 238
              T  A + EP+ G   G VPA   + + +RE+CD +  LLI DEV  G+GRTG L+A 
Sbjct: 196 GPETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFAC 255

Query: 239 MHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVGT----HGTTYGGNPLACAVAG 293
              GV PD+L  AK LG G+ PIGA+L S +    +  G+    HG TY G+P+A A   
Sbjct: 256 EADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGL 315

Query: 294 EVFATINTREVLNGVKQRHQWFCERLN-AINARYGLFK---EIRGLGLLIGCVLK----- 344
            V   +  R    G+ QR     E L+ A+ AR+G      ++RG GL  G  L      
Sbjct: 316 AVVRALLDR----GLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRES 371

Query: 345 ----DEYAGKAKAISNQAAEEGLMIL-IAG------ANVVRFAPALIISEDEVNSGLDRF 393
               D   G A  +   A E GL+   +AG       + +  AP  I+SED++    D+ 
Sbjct: 372 KTPFDPGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHILLAPPFILSEDQIGEITDKL 431

Query: 394 ELACKRFL 401
           E+A  + L
Sbjct: 432 EVALDQVL 439


Lambda     K      H
   0.321    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: 478
Number of extensions: 25
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: 406
Length of database: 440
Length adjustment: 32
Effective length of query: 374
Effective length of database: 408
Effective search space:   152592
Effective search space used:   152592
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