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.
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:
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