GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cstA in Azospirillum brasilense Sp245

Align Carbon starvation protein A (characterized, see rationale)
to candidate AZOBR_RS22555 AZOBR_RS22555 carbon starvation protein CstA

Query= uniprot:A0A0C4Y7X7
         (690 letters)



>FitnessBrowser__azobra:AZOBR_RS22555
          Length = 603

 Score =  439 bits (1128), Expect = e-127
 Identities = 234/562 (41%), Positives = 344/562 (61%), Gaps = 26/562 (4%)

Query: 34  ALWIVVAAICIYLIAYRYYSKFIAEKVMQLDPKRMTPAWRHNDGLDYVPTNKAVLFGHHF 93
           AL  V+A +CI  + YR+Y  F   KV++ D   +TP+    DG +YVPT K V  G HF
Sbjct: 4   ALTFVIATLCILALCYRFYGVFFVRKVLRADDSEVTPSHILADGRNYVPTKKWVNAGQHF 63

Query: 94  AAIAGAGPLVGPVLAAQMGYMPGMLWILAGVVFAGAVQDFMVLFISTRRDGRSLGDLIKS 153
           AAIA AGPLVGPVLAAQ GY+P  LW+L G V  GAV D +VLF S +  G+SL ++ K+
Sbjct: 64  AAIAAAGPLVGPVLAAQFGYLPSFLWLLIGCVIGGAVHDTVVLFASMKHKGQSLSEVAKA 123

Query: 154 EMGTVPGMIALFGCFMIMIIILAVLALIVVKALAGSPWGTFTVGVTIPIALFMGIYTRYI 213
           E+G V G         I+ I +A L+++VV AL  + WG F V +TIPIA+ +G+Y +  
Sbjct: 124 ELGPVAGWCTGLAMLFIITITMAGLSMVVVHALERNAWGAFAVFMTIPIAVALGLYEKI- 182

Query: 214 RPGRIGEVSVIGFVLLMLAIIGGQYVHESAVLAPLFTYDGKALTWMLIIYGFIAAVLPVW 273
             G     + +G   +  ++  G Y+ +  VL    T   + +  +L IY F A  LPVW
Sbjct: 183 -TGSSKGATQVGIAAIAASVFAGPYI-QGTVLGSWLTLHAETVALILPIYAFFATALPVW 240

Query: 274 LLLAPRDYLSTFLKIGTIIALAIGILIVAPELKMPAFTQFAKGGGPVWSGNLFPFLFITI 333
           +LL PR YLS+F+KIG   AL +G++ + PE++ PA T F  GGGPV +G ++PF+ ITI
Sbjct: 241 MLLTPRGYLSSFMKIGVFGALVVGVVFINPEIRFPALTDFIHGGGPVLAGPVWPFISITI 300

Query: 334 ACGAVSGFHALISSGTTPKLLESEAHMRFIGYGAMLAESFVAIMALVAASVIEPGVYFAM 393
           ACGA+SGFHA I SGTTPKL++  + +R + +G MLAE  V +MAL+AA+ + P  YFA+
Sbjct: 301 ACGAISGFHAFIGSGTTPKLIDKWSDIRTVAFGGMLAECVVGVMALIAATSLHPADYFAI 360

Query: 394 N-SPAAVIGTSPESVAQVVSGWGFVITPDVLIQTAKDVGENSIISRAGGAPTLAVGIAHI 452
           N SPAA    +     QVV           L + ++++G + +  R GGA TLAVG+  I
Sbjct: 361 NSSPAAFQALN----MQVVD----------LPRLSQEIGLD-LYGRTGGAVTLAVGMTEI 405

Query: 453 LHQVVGGQAMMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPSFRRTDSLPA 512
             ++     + ++++ F ++FEA+FILTAVD+GTR  R+++QDL G      +R D +P 
Sbjct: 406 FTRIPWFGTLASYFFQFVVMFEAVFILTAVDSGTRVARYLIQDLGGDLYAPLKRLDWVPG 465

Query: 513 NLIATALTVSFWGYFLYQGVVDPLGGINTLWPLFGISNQMLAAVALVLGTCVLVKM-KRG 571
           ++ A+ L    WGY L        G IN++W LFG+SNQ++A+V L++G  +++++ ++ 
Sbjct: 466 SIAASVLACVAWGYLLTS------GDINSVWALFGVSNQLMASVGLIIGATIILRLGQKR 519

Query: 572 QYAWVTLVPTIWLLICTLTAGW 593
            Y    LVP  +L +    AG+
Sbjct: 520 VYMLTCLVPLAYLFVTVNYAGY 541


Lambda     K      H
   0.328    0.141    0.437 

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: 1169
Number of extensions: 58
Number of successful extensions: 6
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: 690
Length of database: 603
Length adjustment: 38
Effective length of query: 652
Effective length of database: 565
Effective search space:   368380
Effective search space used:   368380
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: 54 (25.4 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