Align Carbon starvation protein A (characterized, see rationale)
to candidate Pf6N2E2_5078 Carbon starvation protein A
Query= uniprot:A0A0N9VZ52 (685 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5078 Length = 688 Score = 1264 bits (3270), Expect = 0.0 Identities = 630/682 (92%), Positives = 663/682 (97%) Query: 4 LAKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQL 63 L +HL W +AV+GA AL VVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIAN VMQL Sbjct: 7 LLRHLPWLLLAVVGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANNVMQL 66 Query: 64 DPGRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG 123 D RATPAV+NNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG Sbjct: 67 DARRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG 126 Query: 124 VVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVV 183 VVLAGAVQDFMVLF+STRRNGRSLGDMVREEMGR+PGTIALFGCFLIMIIILAVLALIVV Sbjct: 127 VVLAGAVQDFMVLFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVV 186 Query: 184 KALADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADP 243 KALA+SPWG+FTVMATIPIAMFMG+YMRYIRPGRIGEISV+GVLLLLGSIWLGGQIAADP Sbjct: 187 KALAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISVIGVLLLLGSIWLGGQIAADP 246 Query: 244 VWAKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMP 303 VWAKAF+FTGIQITWMLIGYGFVAAV+PVWLILAPRDYLSTFLKIGTI+ALAIGIL+TMP Sbjct: 247 VWAKAFTFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILVTMP 306 Query: 304 ELKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYI 363 ELKMPALTQF DGTGPVWKGGLFPFLFITIACGAVSGFHALI+SGTTPKLL +E +ARYI Sbjct: 307 ELKMPALTQFTDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNARYI 366 Query: 364 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPEAL 423 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVV VAQTVSSWGF ITPEAL Sbjct: 367 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVAVAQTVSSWGFAITPEAL 426 Query: 424 QAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD 483 QAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD Sbjct: 427 QAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD 486 Query: 484 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLW 543 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVA+WGYLLYQGVIDPLGGINTLW Sbjct: 487 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVALWGYLLYQGVIDPLGGINTLW 546 Query: 544 PLFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAI 603 PLFGISNQMLAGIALML+TVVLIKMKRQRY+WVTLLPA+WLLICTTTAG IKLFDANPAI Sbjct: 547 PLFGISNQMLAGIALMLATVVLIKMKRQRYVWVTLLPASWLLICTTTAGLIKLFDANPAI 606 Query: 604 GFLSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVG 663 GFL+LA+KY+DALA GQ+LAPAK I QMQHV++NAYTNATLT LFLFVVFSILFYA+KVG Sbjct: 607 GFLALARKYNDALAAGQVLAPAKSIEQMQHVVFNAYTNATLTVLFLFVVFSILFYALKVG 666 Query: 664 ISAWGSKERTDKESPFQAIPEA 685 I+AWG+KERTDKE+PFQA+P+A Sbjct: 667 IAAWGTKERTDKEAPFQAVPDA 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: 1636 Number of extensions: 46 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: 685 Length of database: 688 Length adjustment: 39 Effective length of query: 646 Effective length of database: 649 Effective search space: 419254 Effective search space used: 419254 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