GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdhA in Pedobacter sp. GW460-11-11-14-LB5

Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate CA265_RS21785 CA265_RS21785 L-serine ammonia-lyase

Query= uniprot:P33073
         (292 letters)



>FitnessBrowser__Pedo557:CA265_RS21785
          Length = 475

 Score =  136 bits (342), Expect = 1e-36
 Identities = 101/298 (33%), Positives = 149/298 (50%), Gaps = 36/298 (12%)

Query: 5   AREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDVTE 64
           A++++  C   G+K+ ++V+E E+  +  TE E +K +     + H +   +        
Sbjct: 177 AKDLLHWCLSTGLKVSEIVMENEL--AWRTEAETKKGI-----LQHFAVMSDCIYRGCHT 229

Query: 65  YKMIDG---FAKRTYEYANS--GKSIVGDFLAKAMAM-----------------AFSTSE 102
              + G    A+R +       GKS   D+ +   A+                 A + +E
Sbjct: 230 TGFLPGGLNVARRAFPLNKRLIGKSEYSDYNSWVEAIRKGGNGFNYTLDWVSCFALAVNE 289

Query: 103 VNASMGKIVAAPTAGSSGIMPAML---VAATEKYNFDRTTIQNGFLTSIGIGQVITKYAT 159
            NAS G++V APT G++G++PA+L   +   + Y+ ++  I      +  IG +  K AT
Sbjct: 290 ENASFGRVVTAPTNGAAGVIPAVLQYFITFCDGYSEEK--IMQFIACASEIGSIFKKGAT 347

Query: 160 FAGAEGGCQAECGSASAMAAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYP 219
            + A GGCQAE G +SAMAAAAL E LGG+  Q L AA I + + LGL CDPI GLVQ P
Sbjct: 348 ISAAMGGCQAEIGVSSAMAAAALTECLGGSQRQVLMAAEIAMEHHLGLTCDPIGGLVQIP 407

Query: 220 CTFRNASGVINAFISADLALAG--VESLVPFDEVVIAMGEVGNSMIEALRETGLGGLA 275
           C  RN  G I A  ++ LAL     ++ V  D VV  M E    M    +ET  GGLA
Sbjct: 408 CIERNTMGAIKAITASQLALQSNPDKAKVSLDAVVNTMWETALDMNAKYKETSDGGLA 465


Lambda     K      H
   0.317    0.132    0.361 

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: 229
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 292
Length of database: 475
Length adjustment: 30
Effective length of query: 262
Effective length of database: 445
Effective search space:   116590
Effective search space used:   116590
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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