Align Carbon starvation protein A (characterized, see rationale)
to candidate GFF3825 Psest_3894 Carbon starvation protein, predicted membrane protein
Query= uniprot:A0A0C4Y7X7 (690 letters) >FitnessBrowser__psRCH2:GFF3825 Length = 558 Score = 262 bits (670), Expect = 3e-74 Identities = 186/571 (32%), Positives = 286/571 (50%), Gaps = 77/571 (13%) Query: 32 VSALWIVVAAICIYLIAYRYYSKFIAEKVMQLDPKRMTPAWRHNDGLDYVPTNKAVLFGH 91 +SA+ +++ + + Y +YSKFIAE++ +LDP +TPA DG+DYVPTNK VL+GH Sbjct: 1 MSAIALLLVGLIAMALGYVFYSKFIAERIYRLDPHYLTPAHTMRDGVDYVPTNKFVLWGH 60 Query: 92 HFAAIAGAGPLVGPVLAAQMGYMPGMLWILAGVVFAGAVQDFMVLFISTRRDGRSLGDLI 151 HF ++AGA P+VGP +A G+ P W++ G +F V DF L+ S R G+S+G L Sbjct: 61 HFTSVAGAAPIVGPAIAVIWGWGPAFAWVIFGTIFFAGVHDFGALWASARSRGQSVGMLS 120 Query: 152 KSEMGTVPGMIALFGCFMIMIIILAVLALIVVKALAGSPWGTFTVGVTIPIALFMG--IY 209 +G + L F++++++ A ++ L +P V I +AL +G IY Sbjct: 121 GRLIGARGRSLFLVVIFLVLLMVNGAFAAVISNLLVSTPTSVIPVWGAILVALVIGQMIY 180 Query: 210 ---TRYIRPGRIGEVSVIGFVLLMLAIIGGQYVHESAVLAPLFTYDGKALTWMLI--IYG 264 + + P G + VL L ++G QY A+ + K++ W+L+ +Y Sbjct: 181 RYNMKLLWPSLGGVI-----VLYALILLGNQY--PVALPDEIMGLSAKSV-WILLLFVYA 232 Query: 265 FIAAVLPVWLLLAPRDYLSTFLKIGTIIALAIGILIVAPELKMPAFTQFAKGGGPVWSGN 324 IA++LPVW+LL PRDY++ + L + +L APEL PAF Q P + Sbjct: 233 AIASLLPVWVLLQPRDYINGLQLFVGLGLLYLAVLFGAPELVAPAFNQELPADTP----S 288 Query: 325 LFPFLFITIACGAVSGFHALISSGTTPKLLESEAHMRFIGYGAMLAESFVAIMALVAASV 384 + P LF+TIACGA+SGFH L++SGTT K L+ E RF+GY + E +++ A++ + Sbjct: 289 IVPLLFVTIACGAISGFHGLVASGTTSKQLDKETDARFVGYFGAMGEGMLSLAAIICCTA 348 Query: 385 IEPGVYFAMNSPAAVIGTSPESVAQVVSGWGFVITPD-VLIQTAKDVGENSIISRAGGAP 443 GF D + TA G + + GG Sbjct: 349 ------------------------------GFATLTDWQQVYTAFGSGGVTAFVQGGGT- 377 Query: 444 TLAVGIAHILHQVVGGQAMMAFWYHFAILFEALFILTAVDAGTRAGRFMLQ---DLLGSF 500 LA G+ L +GG + AILF T +D G R RF++Q +L G Sbjct: 378 LLANGLG--LPAELGGTILAV----MAILFAG----TTMDTGLRLQRFVIQEAGELAGMK 427 Query: 501 VPSFRRTDSLPANLIATALTVSFWGYFLYQGVVDPLGGINTLWPLFGISNQMLAAVALVL 560 V + LI T + V + D GG+ +WPLFG +NQ+LA + L + Sbjct: 428 VNT----------LIGTLIAVGVCMALAFGAGSDGTGGM-VIWPLFGTTNQLLAGLTLAV 476 Query: 561 GTCVLVKMKRGQYAWVTLVPTIWLLICTLTA 591 T +L+K+ G+ TLVP ++LL ++ A Sbjct: 477 ITVILIKL--GRSPLYTLVPLVFLLAMSIYA 505 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: 1121 Number of extensions: 66 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 690 Length of database: 558 Length adjustment: 37 Effective length of query: 653 Effective length of database: 521 Effective search space: 340213 Effective search space used: 340213 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