GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Escherichia coli BW25113

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 16752 b2662 4-aminobutyrate aminotransferase (NCBI)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__Keio:16752
          Length = 426

 Score =  218 bits (556), Expect = 2e-61
 Identities = 149/399 (37%), Positives = 203/399 (50%), Gaps = 46/399 (11%)

Query: 30  RGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVS-NVFTNEPALR 88
           R    RVWD  GRE +DFAGGIAV   GH HP +VAA+  Q  KL H    V   EP L 
Sbjct: 29  RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88

Query: 89  LA---HKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRT 145
           L    ++ V   FA++     +G+EA E A K+AR  A  R GT     +A   ++HGRT
Sbjct: 89  LCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR-AATKRSGT-----IAFSGAYHGRT 142

Query: 146 LFTVNVGGQ-SKYSDGFG---------------------PKITGITHVPYNDLAALKAAV 183
            +T+ + G+ + YS G G                       I  I  +  ND      A 
Sbjct: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKND------AA 196

Query: 184 SDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQH 243
            +   A+V+EP+QGEGG   +  +++Q  R LCD H  +L+ DEVQ+G GR+G LFA + 
Sbjct: 197 PEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQ 256

Query: 244 YGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVIN 303
            GV PD+ T AKS+ GGFP+A +    ++   +  G  G TY GNP+AC  A  V+ V  
Sbjct: 257 MGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFE 316

Query: 304 TPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVL---SDAWKGKAK---DI 357
              +L   N    K K  L  I EK+    +VRGLG ++   L    D  K  AK   +I
Sbjct: 317 QENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEI 376

Query: 358 FNAAEREGLMILQAGP--DVIRFAPSLVVEDADIDAGLD 394
              A  +GL++L  GP  +V+R    L +EDA I  GL+
Sbjct: 377 VARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415


Lambda     K      H
   0.320    0.136    0.400 

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: 430
Number of extensions: 20
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: 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