GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Skermanella stibiiresistens SB22

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_051511316.1 N825_RS00145 ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_000576635.1:WP_051511316.1
          Length = 269

 Score =  246 bits (627), Expect = 5e-70
 Identities = 126/250 (50%), Positives = 173/250 (69%), Gaps = 10/250 (4%)

Query: 22  AIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIV 81
           A+ +  ++K +GQ  VL+ ++L  H G+ I + G SGSGKST +RCIN LE    G++ V
Sbjct: 20  AVVVEDLHKRFGQLEVLKGVSLVAHEGDVISMIGSSGSGKSTFLRCINLLETPDEGRVWV 79

Query: 82  DGI----------ELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131
           +G            + +D K +D++RS +GMVFQ FNL+ H+T+L+N+  AP+ V  VPK
Sbjct: 80  NGELIRMKQGRHHAVPADAKQVDRIRSGLGMVFQGFNLWTHMTVLQNVIEAPVHVLGVPK 139

Query: 132 REAEETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPE 191
            EA + A   L+KV +  +A  YP  LSGGQQQRVAIAR+L M+PK+MLFDEPTSALDPE
Sbjct: 140 AEAIDRAEALLQKVGLEAKASSYPSHLSGGQQQRVAIARALAMQPKVMLFDEPTSALDPE 199

Query: 192 MIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSE 251
           ++ EVL  M QLA+EGMTM+ VTHEMGFA+ V++ VIF+  G+I EQ  P     NP+S+
Sbjct: 200 LVGEVLRVMRQLADEGMTMIIVTHEMGFAREVSSEVIFLHQGRIEEQGPPDQVLANPRSD 259

Query: 252 RTKQFLSQIL 261
           R +QFL++ L
Sbjct: 260 RCRQFLARNL 269


Lambda     K      H
   0.320    0.134    0.391 

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: 212
Number of extensions: 10
Number of successful extensions: 2
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: 263
Length of database: 269
Length adjustment: 25
Effective length of query: 238
Effective length of database: 244
Effective search space:    58072
Effective search space used:    58072
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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