GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Azospirillum brasilense Sp245

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__azobra:AZOBR_RS30410
          Length = 371

 Score =  271 bits (692), Expect = 3e-77
 Identities = 143/274 (52%), Positives = 187/274 (68%), Gaps = 11/274 (4%)

Query: 21  VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80
           +KD +LDI+  EF  F+GPSGCGKTT LR+IAG      G + IG R ++ +P   RD+ 
Sbjct: 34  LKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIGGRDISGLPAHKRDVG 93

Query: 81  MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140
           MVFQ+YAL+PHMTV +N+AFGL+ R+VP+AEI+RRV  A  ++ + HL DR+P  LSGGQ
Sbjct: 94  MVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGLKHLADRRPSQLSGGQ 153

Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200
           +QRVAL R IV EP+V L+DEPLSNLDAKLRVQMR E+  L ++L  T I+VTHDQ EA 
Sbjct: 154 QQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKLGLTTIFVTHDQEEAN 213

Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEI-VQDGDAFYFRA 259
           T+ DRI VM DG++QQ  TPQ +Y  P N+FVAGF+G+   N + G++   DG   +   
Sbjct: 214 TICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANVLEGQVRAVDGGTAFVMG 271

Query: 260 PSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293
             + + LP G        GA GK   L  RP++L
Sbjct: 272 GGVPIPLPHG-----VEPGAAGK---LMFRPQNL 297


Lambda     K      H
   0.321    0.138    0.395 

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: 410
Number of extensions: 12
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: 384
Length of database: 371
Length adjustment: 30
Effective length of query: 354
Effective length of database: 341
Effective search space:   120714
Effective search space used:   120714
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