GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Thiothrix lacustris DSM 21227

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  150 bits (379), Expect = 3e-41
 Identities = 87/243 (35%), Positives = 133/243 (54%), Gaps = 18/243 (7%)

Query: 2   IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61
           +ELKNV+KYYG  H +K ++L ++ GE +V +GPSG GKST +R + GLE ++ G+++++
Sbjct: 4   LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63

Query: 62  NLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLA-------PMKLQKKSKKEAEE 114
              +    ++   ++  AMVFQ + LYPHMTV +N++ A       P  +Q+K K  A++
Sbjct: 64  GRDI---TEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120

Query: 115 TAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEV 174
                L +   L +    P  LSGGQ+QRVAI RS+       LFDEP S LD       
Sbjct: 121 -----LNLTAYLQRT---PKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNT 172

Query: 175 LDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARL 234
              +  +  +   T V VTH+   A  +ADR++ + DG I +   P E +  P       
Sbjct: 173 RVEIASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVAR 232

Query: 235 FLG 237
           F+G
Sbjct: 233 FIG 235


Lambda     K      H
   0.317    0.133    0.372 

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: 170
Number of extensions: 8
Number of successful extensions: 3
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: 242
Length of database: 348
Length adjustment: 26
Effective length of query: 216
Effective length of database: 322
Effective search space:    69552
Effective search space used:    69552
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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