GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Azospirillum brasilense Sp245

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate AZOBR_RS08665 AZOBR_RS08665 amino acid ABC transporter permease

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__azobra:AZOBR_RS08665
          Length = 367

 Score =  269 bits (688), Expect = 9e-77
 Identities = 166/432 (38%), Positives = 232/432 (53%), Gaps = 68/432 (15%)

Query: 4   TSFVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHG 63
           T  V T  +     P + VG + W+R NLF+   N  LT+       WL+  A P LL  
Sbjct: 2   TDNVHTGSIPDERPPANTVGPVAWLRNNLFNTWYNALLTIL----IAWLLFKAIPPLLDW 57

Query: 64  -VWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFL 122
            +++ANS      +  +  G     ACW  +  +    +FG +P D+ WR  +T   + +
Sbjct: 58  LIFSANSFGTPPQVCRQEGG-----ACWTFVSEKLRFVMFGTFPYDEQWRPLIT---IVI 109

Query: 123 ALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPKLGV 182
            +A VL     R             FW  W   +W     +AG   +G+L        GV
Sbjct: 110 IIALVLASCDRR-------------FWKPWLALVW-----IAGLTAVGVLMWG-----GV 146

Query: 183 PVSAGIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSL 242
                                          L L  V++  +GG  L L++ V  + V+ 
Sbjct: 147 -------------------------------LGLTYVENTLWGGLPLTLMLSVVGLSVAF 175

Query: 243 PLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRV 302
           P  +LLALGR+S +  ++ +SV  IE +RGVPLI+LLF AS++   FLP G NFD +LR 
Sbjct: 176 PASVLLALGRRSQLPAIRVISVTYIELIRGVPLISLLFMASVMFPLFLPTGVNFDKLLRA 235

Query: 303 VILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVS 362
            I   +FAAAY+AE IRGGL A+P+GQYEAADALGL+YWQA   II+PQAL ISIP +V+
Sbjct: 236 QIAFIMFAAAYMAEAIRGGLQAIPKGQYEAADALGLNYWQAMGKIILPQALAISIPPLVN 295

Query: 363 SFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYS 422
           +FI  FKDT+LV  +GL+D L G +    SD AW+G Y E Y+F+ +I+++F +SMS+YS
Sbjct: 296 TFISFFKDTSLVIIIGLYD-LLGTAKAALSDPAWRGFYREAYLFIGVIYWVFCYSMSKYS 354

Query: 423 MYLERKLKRDHR 434
             LER L+R HR
Sbjct: 355 QKLERDLRRGHR 366


Lambda     K      H
   0.329    0.143    0.457 

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: 590
Number of extensions: 41
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: 434
Length of database: 367
Length adjustment: 31
Effective length of query: 403
Effective length of database: 336
Effective search space:   135408
Effective search space used:   135408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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