Align Carbon starvation protein A (characterized, see rationale)
to candidate Echvi_0765 Echvi_0765 Carbon starvation protein, predicted membrane protein
Query= uniprot:A0A0C4Y7X7 (690 letters) >FitnessBrowser__Cola:Echvi_0765 Length = 544 Score = 265 bits (677), Expect = 4e-75 Identities = 181/557 (32%), Positives = 280/557 (50%), Gaps = 70/557 (12%) Query: 37 IVVAAICIYLIAYRYYSKFIAEKVMQLDPKRMTPAWRHNDGLDYVPTNKAVLFGHHFAAI 96 +++AAI + + AY Y KF+ +K + +TP+ ++ DG+DY P+ V+ GHHFA+I Sbjct: 7 LLLAAITL-IAAYFIYGKFVFKK-FDIRNSHVTPSHKYQDGVDYEPSRPIVVLGHHFASI 64 Query: 97 AGAGPLVGPVLAAQMGYMPGMLWILAGVVFAGAVQDFMVLFISTRRDGRSLGDLIKSEMG 156 AGAGP+VGP++A G++P ++WIL G +F GAV D + S R +G+S+G +IK +G Sbjct: 65 AGAGPIVGPIIAVTFGWIPAVIWILVGGIFFGAVHDLGSMVASLRSEGKSIGTIIKQNIG 124 Query: 157 TVPGMIALFGCFMIMIIILAVLALIVVKALAGSPWGTFTVGVTIPIALFMGIYTRYI--R 214 + + F +I+++AV A I+ K +P + I +A+ G+ + + R Sbjct: 125 QSGKQLFMLFSFSTLILVIAVFADIIAKTFINNPGVASASILFILLAIVFGLINKMVAHR 184 Query: 215 PGRIGEVSVIGFVLLMLAIIGGQYVHESAVLAPLFTYDGKALTWMLIIYGFIAAVLPVWL 274 SV+G L+ + G + F D K ++L+ Y FIA+V PV L Sbjct: 185 KSLFLLTSVVGVGLMYYFVYLGMQLP--------FELDYKVWLYVLLAYAFIASVTPVSL 236 Query: 275 LLAPRDYLSTFLKIGTIIALAIGILIVAPELKMPAFTQFAKGGGPVWSGNLFPFLFITIA 334 LL PRDYL++FL G II +GI P++KM A G LFP LF+TIA Sbjct: 237 LLQPRDYLNSFLLYGLIIFAVLGIFYANPDIKMDHQIHLASDN----LGYLFPVLFVTIA 292 Query: 335 CGAVSGFHALISSGTTPKLLESEAHMRFIGYGAMLAESFVAIMALVAASVIEPGVYFAMN 394 CGA+SGFH+L++SGTT K ++ E + +G+G ML ESF+AI+++ Sbjct: 293 CGAISGFHSLVASGTTSKQIDKEGDAKIVGFGGMLIESFLAIISV--------------- 337 Query: 395 SPAAVIGTSPESVAQVVSGWGFVITPDVLIQTAKDVGENSIISRAGGAPTLAVGIAHILH 454 AVI S E +S G V ++ S GA ++GI L Sbjct: 338 --GAVIILSREEYTMALSAKGPV----------------TMFSDGLGAMMASLGIPEELA 379 Query: 455 QVVGGQAMMAFWYHFAILFEALFILTAVDAGTRAGRFMLQDLLGSFVPSFRRTDSLPANL 514 F L + F LT +D TR RF Q+ +T + Sbjct: 380 ------------VSFVALTVSAFALTTLDTCTRLARFTFQEYFEGAKGPVGKTFA-SNRY 426 Query: 515 IATALTVSFWGYFLYQGVVDPLGGINTLWPLFGISNQMLAAVALVLGTCVLVKMKRGQYA 574 I+T++ V + ++ GG TLWP+FG +NQ+LAA+AL+ L+ K+ A Sbjct: 427 ISTSIVV------ILSILLISSGGFTTLWPIFGSANQLLAALALLAVAVWLI--KKNVNA 478 Query: 575 WVTLVPTIWLLICTLTA 591 ++P ++ TLT+ Sbjct: 479 TFVIIPMFFMFTVTLTS 495 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: 920 Number of extensions: 46 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: 1 Length of query: 690 Length of database: 544 Length adjustment: 37 Effective length of query: 653 Effective length of database: 507 Effective search space: 331071 Effective search space used: 331071 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: 53 (25.0 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