GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Pseudomonas stutzeri RCH2

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type

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



>FitnessBrowser__psRCH2:GFF3586
          Length = 426

 Score =  213 bits (543), Expect = 7e-60
 Identities = 142/403 (35%), Positives = 213/403 (52%), Gaps = 40/403 (9%)

Query: 16  PVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75
           P++A  A      + S + D +G+E+IDFAGGIAV   GH HP+++KA+ +Q  K  HT 
Sbjct: 25  PIFADHA------KNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTC 78

Query: 76  -NGYTNEPVLRLAKQL---IDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131
                 EP + L +++   +   FA +     +G+EA E A+K+AR        + ++G+
Sbjct: 79  FQVLAYEPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARA------ATGRAGV 132

Query: 132 VAFKNAFHGRTLFTVSAGGQPA-YSQDFAPLPPQIQHAIYN------DLDSAKALIDD-- 182
           +AF  A+HGRT+ T+   G+ A YS     +P  I  A+Y        +D + A I+   
Sbjct: 133 IAFTGAYHGRTMMTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIYGVSVDDSIASIERIF 192

Query: 183 -------NTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGEL 235
                  +  A+I+EP+QGEGG   A  DF+  LR LCD H  LLI DEVQTG GRTG  
Sbjct: 193 KNDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLIADEVQTGAGRTGTF 252

Query: 236 YAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEV 295
           +A    GV  DL + AK++GGGFPI  +         +  G  G TY GNPL+CA A  V
Sbjct: 253 FAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAV 312

Query: 296 FATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKD--EYAGKAKA 353
                  ++L+  K   +     L AI  ++    E+RGLG +I   L +  ++A  A A
Sbjct: 313 LEVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMIAIELFEDGDHARPAAA 372

Query: 354 ISNQ----AAEEGLMILIAGA--NVVRFAPALIISEDEVNSGL 390
           +++Q    A ++GL++L  G   NV+R    L   ++ ++ GL
Sbjct: 373 LTSQIVARARDKGLILLSCGTYYNVLRVLVPLTAEDELLDRGL 415


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: 460
Number of extensions: 21
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: 406
Length of database: 426
Length adjustment: 31
Effective length of query: 375
Effective length of database: 395
Effective search space:   148125
Effective search space used:   148125
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