Align Carbon starvation protein A (characterized, see rationale)
to candidate N515DRAFT_4411 N515DRAFT_4411 carbon starvation protein
Query= uniprot:A0A0N9VZ52 (685 letters) >FitnessBrowser__Dyella79:N515DRAFT_4411 Length = 691 Score = 902 bits (2332), Expect = 0.0 Identities = 422/681 (61%), Positives = 547/681 (80%), Gaps = 3/681 (0%) Query: 5 AKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQLD 64 A + W A+A++GA+ L VVALRRGE INA+W+V AA+A++++ YR+YS FI V+++D Sbjct: 11 AGKILWAAIAIVGAWCLGVVALRRGEPINAIWLVAAAIAVFVIGYRFYSRFIDTYVLRMD 70 Query: 65 PGRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGV 124 P RATPAV+ NDGLDYVPT+K ++FGHHFAAIAGAGPLVGPVLAAQMGYLPGTLW++ GV Sbjct: 71 PSRATPAVLRNDGLDYVPTDKWVVFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWILFGV 130 Query: 125 VLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVVK 184 V AGAVQDFM+L +S RR+GRSLG+M+R+E+G V G +A+FG ++M+I+LAVLAL+VVK Sbjct: 131 VFAGAVQDFMILGLSVRRDGRSLGNMLRDELGPVAGIVAMFGVLVLMMIVLAVLALVVVK 190 Query: 185 ALADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADPV 244 AL SPWG +TV TIPIA+ MG+Y+RYIRPG+I E+S+VG++LLL +IW G +AA P Sbjct: 191 ALTHSPWGTYTVACTIPIALLMGIYLRYIRPGKILEVSIVGLILLLLAIWSGAYVAASPA 250 Query: 245 WAKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMPE 304 WA AF F + W+LI YGF A+V+PVWL+LAPRDYLSTFLKIGTI LA+ I + P Sbjct: 251 WAAAFDFDAKALAWLLIAYGFCASVLPVWLLLAPRDYLSTFLKIGTIALLALAIFLAAPT 310 Query: 305 LKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYIG 364 L+MPALT+F+DGTGPV++G LFPFLFITIACGAVSG+H++I+SGTTPKLL++EG AR +G Sbjct: 311 LQMPALTKFVDGTGPVFQGNLFPFLFITIACGAVSGWHSIISSGTTPKLLSNEGEARMVG 370 Query: 365 YGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPEALQ 424 YGGMLME+FVAIMA++AA+ + PGVYFAMNSPAA++G A +S WGF+++P+ L Sbjct: 371 YGGMLMEAFVAIMALIAAASMHPGVYFAMNSPAALIGTTAQSAATAISQWGFVVSPDELL 430 Query: 425 AVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVDA 484 A++IGE+++L+RAGGAPTLAVG+AQ+LH ++PGE MAFWYH+AILFEALFILT VDA Sbjct: 431 NTARNIGESSILSRAGGAPTLAVGMAQLLHGIIPGEGMMAFWYHYAILFEALFILTTVDA 490 Query: 485 GTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLWP 544 GTR GRFM+Q++ G LK TESWT NLIATA CV +WGY LYQG +DPLGGINTLWP Sbjct: 491 GTRVGRFMIQEIAGLIHEPLKHTESWTGNLIATAICVGLWGYFLYQGAVDPLGGINTLWP 550 Query: 545 LFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAIG 604 LFGI+NQMLA +ALML+TVV +K+KR+RY+WV +PA WL++CT TAG+ KL +I Sbjct: 551 LFGIANQMLAAVALMLATVVTVKLKRERYVWVPGIPAIWLVVCTLTAGYYKLVG---SIS 607 Query: 605 FLSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVGI 664 F + A+KY+ A A G++LAPAK + +MQ ++ N Y +A LT +F+ +V ++ +AI + Sbjct: 608 FTAAAQKYAAAAAEGKLLAPAKSVAEMQRIVTNNYVDAALTGIFMLLVVTMAGFAINAIL 667 Query: 665 SAWGSKERTDKESPFQAIPEA 685 AW T E P+ A+ A Sbjct: 668 KAWRVNHPTAHEEPYVALEGA 688 Lambda K H 0.328 0.141 0.433 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: 1394 Number of extensions: 52 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: 685 Length of database: 691 Length adjustment: 39 Effective length of query: 646 Effective length of database: 652 Effective search space: 421192 Effective search space used: 421192 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 (21.7 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