Align Carbon starvation protein A (characterized, see rationale)
to candidate AZOBR_RS18105 AZOBR_RS18105 carbon starvation protein A
Query= uniprot:A0A0C4Y7X7 (690 letters) >FitnessBrowser__azobra:AZOBR_RS18105 Length = 688 Score = 993 bits (2567), Expect = 0.0 Identities = 482/678 (71%), Positives = 571/678 (84%) Query: 1 MNRIGQHLVWLAVAILGAFAFATVALSRGEAVSALWIVVAAICIYLIAYRYYSKFIAEKV 60 M RI H WL +A+LGAFA TVAL+RGE ++ALW+VVAA+C YL++YRYYS FIA +V Sbjct: 1 MPRILNHAPWLVLAVLGAFALGTVALARGETINALWLVVAAVCTYLVSYRYYSLFIATRV 60 Query: 61 MQLDPKRMTPAWRHNDGLDYVPTNKAVLFGHHFAAIAGAGPLVGPVLAAQMGYMPGMLWI 120 M+LDP R TPA RHNDGLDYVPTN+ VLFGHHFAAIAGAGPLVGPVLAAQMGY+PGMLWI Sbjct: 61 MRLDPARPTPAMRHNDGLDYVPTNQYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMLWI 120 Query: 121 LAGVVFAGAVQDFMVLFISTRRDGRSLGDLIKSEMGTVPGMIALFGCFMIMIIILAVLAL 180 LAGVV AGAVQDFM+LF+S RRDGRSLG+LIK+E+G +PG+IALFG FMIM+IILAVLAL Sbjct: 121 LAGVVVAGAVQDFMILFVSMRRDGRSLGELIKAELGDIPGVIALFGTFMIMVIILAVLAL 180 Query: 181 IVVKALAGSPWGTFTVGVTIPIALFMGIYTRYIRPGRIGEVSVIGFVLLMLAIIGGQYVH 240 +VVKAL SPWG FTV T+PIALFMGIY R++RPGRIGE+S+IGF LL+ AI+ G V Sbjct: 181 VVVKALTNSPWGFFTVAATVPIALFMGIYMRFLRPGRIGEISIIGFFLLIAAILLGGQVA 240 Query: 241 ESAVLAPLFTYDGKALTWMLIIYGFIAAVLPVWLLLAPRDYLSTFLKIGTIIALAIGILI 300 +S AP+FT G +TW+LI YGF+A+VLPVWLLLAPRDYLSTFLK+GTI+ LA+ IL+ Sbjct: 241 QSETWAPVFTLTGVQITWILIGYGFVASVLPVWLLLAPRDYLSTFLKVGTIVMLALCILL 300 Query: 301 VAPELKMPAFTQFAKGGGPVWSGNLFPFLFITIACGAVSGFHALISSGTTPKLLESEAHM 360 VAP +KMP+ T+F G GPVWSG+LFPFLFITIACGAVSGFHALISSGTTPK++E+E H Sbjct: 301 VAPPMKMPSVTRFIDGTGPVWSGSLFPFLFITIACGAVSGFHALISSGTTPKMVENELHT 360 Query: 361 RFIGYGAMLAESFVAIMALVAASVIEPGVYFAMNSPAAVIGTSPESVAQVVSGWGFVITP 420 RFIGYG ML ESFVA+MALVAAS IEPG+YFAMNSP A++GT+ ES AQV++ WGFVITP Sbjct: 361 RFIGYGGMLTESFVAVMALVAASCIEPGIYFAMNSPPALLGTTAESAAQVINNWGFVITP 420 Query: 421 DVLIQTAKDVGENSIISRAGGAPTLAVGIAHILHQVVGGQAMMAFWYHFAILFEALFILT 480 +++ QTA+DVGE SI+SRAGGAPTLAVG+A I ++ GG+ MMAFWYHFAILFEALFILT Sbjct: 421 EMITQTAQDVGEVSILSRAGGAPTLAVGMAQIFSELFGGKGMMAFWYHFAILFEALFILT 480 Query: 481 AVDAGTRAGRFMLQDLLGSFVPSFRRTDSLPANLIATALTVSFWGYFLYQGVVDPLGGIN 540 AVDAGTRAGRFMLQDLLG F +RT S NLIAT L V+ WGY LYQGVVDPLGGIN Sbjct: 481 AVDAGTRAGRFMLQDLLGVFFKPLQRTASWAGNLIATGLCVAAWGYILYQGVVDPLGGIN 540 Query: 541 TLWPLFGISNQMLAAVALVLGTCVLVKMKRGQYAWVTLVPTIWLLICTLTAGWQKLFDAD 600 T WPLFGISNQMLA +AL+L T VL +MKR +YAWVT+VP WLLICTLTAG QK+F ++ Sbjct: 541 TFWPLFGISNQMLAGIALILATVVLFRMKRERYAWVTMVPAAWLLICTLTAGVQKVFHSN 600 Query: 601 PKVSFLTHAAKFSDAIAQGKVLAPAKSMEQMHRIVFNDYLDAGLCALFMFVVLSIVFYGF 660 P + FL HA +FS A +G++LAPA SMEQM +++FNDYLDA L +LF+ VVL+++ +G Sbjct: 601 PAIGFLAHAERFSTAANEGRLLAPATSMEQMRQVIFNDYLDAALASLFVLVVLAVLVFGV 660 Query: 661 KTAMKARAENRPTDRETP 678 + +KA +RPT RE P Sbjct: 661 LSCLKALRSDRPTTREIP 678 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: 1523 Number of extensions: 68 Number of successful extensions: 4 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: 688 Length adjustment: 39 Effective length of query: 651 Effective length of database: 649 Effective search space: 422499 Effective search space used: 422499 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