GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Azospirillum brasilense Sp245

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__azobra:AZOBR_RS30410
          Length = 371

 Score =  244 bits (623), Expect = 3e-69
 Identities = 142/331 (42%), Positives = 196/331 (59%), Gaps = 14/331 (4%)

Query: 4   LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63
           + I  +   YG    LK I + ++ GEF   LG SGCGK+TLL +IAG      G + IG
Sbjct: 19  VRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIG 78

Query: 64  ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123
            R + G+    RD+ MVFQSYAL+P+++V RN+ FGLE RRVP+AE ++ V     L+ +
Sbjct: 79  GRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGL 138

Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183
           ++L DR+PSQLSGGQ+QRVA+ R +V  P+V L DEPLSNLDAKLR++MR EL  L + L
Sbjct: 139 KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKL 198

Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243
             T ++VTHDQ EA T+  RIAVM DG ++Q+  P E+YD PA L+VAGF+G+   N+L+
Sbjct: 199 GLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANVLE 256

Query: 244 AEMTA---NGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQ-----R 295
            ++ A       + G    +PLP      A AG   K+  RP+ L +            R
Sbjct: 257 GQVRAVDGGTAFVMGGGVPIPLPHGVEPGA-AG---KLMFRPQNLFIRQDGGPPRAGHVR 312

Query: 296 LTASVEVVELTGPELVTTATVGSQRITACLP 326
           L   V   E  G  +     +G Q++    P
Sbjct: 313 LMGVVRHREFLGASIRYAVDIGGQQVQVDAP 343


Lambda     K      H
   0.320    0.136    0.385 

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: 338
Number of extensions: 18
Number of successful extensions: 1
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: 360
Length of database: 371
Length adjustment: 30
Effective length of query: 330
Effective length of database: 341
Effective search space:   112530
Effective search space used:   112530
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: 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