Align Carbon starvation protein A (characterized, see rationale)
to candidate HSERO_RS09795 HSERO_RS09795 carbon starvation protein A
Query= uniprot:A0A0C4Y7X7 (690 letters) >FitnessBrowser__HerbieS:HSERO_RS09795 Length = 689 Score = 1072 bits (2772), Expect = 0.0 Identities = 526/689 (76%), Positives = 611/689 (88%), Gaps = 1/689 (0%) Query: 1 MNRIGQHLVWLAVAILGAFAFATVALSRGEAVSALWIVVAAICIYLIAYRYYSKFIAEKV 60 MNRI L WLA+A+ GA A A VAL RGE+++A+W+VVAA+C+YLIAYR+YSKFIA++V Sbjct: 1 MNRIVSRLGWLALALAGAGACAYVALQRGESINAVWLVVAAVCVYLIAYRFYSKFIADRV 60 Query: 61 MQLDPKRMTPAWRHNDGLDYVPTNKAVLFGHHFAAIAGAGPLVGPVLAAQMGYMPGMLWI 120 + LD RMTPA++ NDGLDYVPTNK VLFGHHFAAIAGAGPLVGPVLAAQMGY+PGMLWI Sbjct: 61 LGLDGGRMTPAYKFNDGLDYVPTNKYVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGMLWI 120 Query: 121 LAGVVFAGAVQDFMVLFISTRRDGRSLGDLIKSEMGTVPGMIALFGCFMIMIIILAVLAL 180 LAGVVFAGAVQDFMVLFISTRRDGRSLGDLIKSE+G VPG+IALFG FMIM+IILAVLAL Sbjct: 121 LAGVVFAGAVQDFMVLFISTRRDGRSLGDLIKSELGQVPGVIALFGAFMIMVIILAVLAL 180 Query: 181 IVVKALAGSPWGTFTVGVTIPIALFMGIYTRYIRPGRIGEVSVIGFVLLMLAIIGGQYVH 240 IVVKALA SPWG+FTV TIPIALFMG+Y+RYIRPGRIGEVS IGFVLLMLAI+GGQYV Sbjct: 181 IVVKALAESPWGSFTVAATIPIALFMGVYSRYIRPGRIGEVSWIGFVLLMLAIVGGQYVQ 240 Query: 241 ESAVLAPLFTYDGKALTWMLIIYGFIAAVLPVWLLLAPRDYLSTFLKIGTIIALAIGILI 300 E L +FT+DGK LTWMLI YGF+A+VLPVWLLLAPRDYLSTFLKIGTI+ALA+GI+ Sbjct: 241 EHPALGQMFTFDGKQLTWMLIGYGFVASVLPVWLLLAPRDYLSTFLKIGTILALALGIVF 300 Query: 301 VAPELKMPAFTQFAKGGGPVWSGNLFPFLFITIACGAVSGFHALISSGTTPKLLESEAHM 360 +AP LKM A T+F G GPVWSG+LFPFLFITIACGAVSGFHALISSGTTPKLLE+E H Sbjct: 301 IAPHLKMHAVTRFIDGSGPVWSGSLFPFLFITIACGAVSGFHALISSGTTPKLLENEKHA 360 Query: 361 RFIGYGAMLAESFVAIMALVAASVIEPGVYFAMNSPAAVIGTSPESVAQVVSGWGFVITP 420 RFIGYGAML ESFVAIMAL+AAS IEPG+YFAMNSPAA+IGT+PE+VAQV+S WGF ITP Sbjct: 361 RFIGYGAMLMESFVAIMALIAASCIEPGIYFAMNSPAALIGTTPENVAQVISQWGFHITP 420 Query: 421 DVLIQTAKDVGENSIISRAGGAPTLAVGIAHILHQVVGGQAMMAFWYHFAILFEALFILT 480 ++L TA+ VGE++IISRAGGAPTLAVG+A IL V G+AMMAFWYHFAILFEALFILT Sbjct: 421 EMLTHTAQAVGEHTIISRAGGAPTLAVGMAQILSGVT-GEAMMAFWYHFAILFEALFILT 479 Query: 481 AVDAGTRAGRFMLQDLLGSFVPSFRRTDSLPANLIATALTVSFWGYFLYQGVVDPLGGIN 540 AVDAGTRAGRFMLQDLLG+F+P +RTDS A+LIAT L V+ WGYFLYQGVVDPLGGIN Sbjct: 480 AVDAGTRAGRFMLQDLLGAFIPPMKRTDSWVASLIATGLCVAGWGYFLYQGVVDPLGGIN 539 Query: 541 TLWPLFGISNQMLAAVALVLGTCVLVKMKRGQYAWVTLVPTIWLLICTLTAGWQKLFDAD 600 TLWPLFGISNQMLA +AL+L TCVL KMKR ++AWVT++PT WLL CTLTAGWQK+FDA+ Sbjct: 540 TLWPLFGISNQMLAGIALILATCVLFKMKRDRFAWVTVLPTAWLLACTLTAGWQKVFDAN 599 Query: 601 PKVSFLTHAAKFSDAIAQGKVLAPAKSMEQMHRIVFNDYLDAGLCALFMFVVLSIVFYGF 660 P+V FL HA+K+ A+ +GK+LAPAKS+EQM +++FNDY+DAGL A+FM VV+S++ +G Sbjct: 600 PRVGFLAHASKYQAALDEGKLLAPAKSIEQMRQVIFNDYVDAGLAAMFMLVVISVLVFGI 659 Query: 661 KTAMKARAENRPTDRETPFEPMPASASAQ 689 +T +KAR+ ++P+ +E P+E +PASA AQ Sbjct: 660 RTVLKARSAHQPSVKEAPYETLPASALAQ 688 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: 1495 Number of extensions: 51 Number of successful extensions: 3 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: 689 Length adjustment: 39 Effective length of query: 651 Effective length of database: 650 Effective search space: 423150 Effective search space used: 423150 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