Align Carbon starvation protein A (characterized, see rationale)
to candidate PfGW456L13_1444 Carbon starvation protein A
Query= uniprot:A0A0N9VZ52 (685 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1444 Length = 688 Score = 1272 bits (3291), Expect = 0.0 Identities = 634/680 (93%), Positives = 662/680 (97%) Query: 6 KHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQLDP 65 +HL W +A++GA AL VVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIAN VMQLD Sbjct: 9 RHLPWLVLAIVGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANNVMQLDA 68 Query: 66 GRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV 125 RATPAV+NNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV Sbjct: 69 RRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVV 128 Query: 126 LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVVKA 185 LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGR+PGTIALFGCFLIMIIILAVLALIVVKA Sbjct: 129 LAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVVKA 188 Query: 186 LADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADPVW 245 LA+SPWG+FTVMATIPIAMFMG+YMRYIRPGRIGEISV+GVLLLLGSIWLGGQIAADPVW Sbjct: 189 LAESPWGIFTVMATIPIAMFMGIYMRYIRPGRIGEISVIGVLLLLGSIWLGGQIAADPVW 248 Query: 246 AKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMPEL 305 AKAFSFTGIQITWMLIGYGFVAAV+PVWLILAPRDYLSTFLKIGTI+ALAIGIL+TMPEL Sbjct: 249 AKAFSFTGIQITWMLIGYGFVAAVLPVWLILAPRDYLSTFLKIGTIVALAIGILVTMPEL 308 Query: 306 KMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYIGY 365 KMPALTQF+DGTGPVWKGGLFPFLFITIACGAVSGFHALI+SGTTPKLL +E +ARYIGY Sbjct: 309 KMPALTQFVDGTGPVWKGGLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNARYIGY 368 Query: 366 GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPEALQA 425 GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAA+VGGDVV VA VS+WGF ITPEALQA Sbjct: 369 GGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAVVGGDVVAVATAVSNWGFAITPEALQA 428 Query: 426 VAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVDAG 485 VA DIGETT+LARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVDAG Sbjct: 429 VAHDIGETTILARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVDAG 488 Query: 486 TRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLWPL 545 TRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWG+LLYQGVIDPLGGINTLWPL Sbjct: 489 TRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGWLLYQGVIDPLGGINTLWPL 548 Query: 546 FGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAIGF 605 FGISNQMLAGIALML TVVLIKMKRQRY+WVT+LPA WLLICTTTAGFIKLFDANPAIGF Sbjct: 549 FGISNQMLAGIALMLGTVVLIKMKRQRYVWVTMLPAVWLLICTTTAGFIKLFDANPAIGF 608 Query: 606 LSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVGIS 665 LSLAKKYSDALANGQILAPAKDITQMQHVI+NAYTNATLTALFLFVVFSILFYA+KVGI+ Sbjct: 609 LSLAKKYSDALANGQILAPAKDITQMQHVIFNAYTNATLTALFLFVVFSILFYALKVGIA 668 Query: 666 AWGSKERTDKESPFQAIPEA 685 AWG KERTDKESPFQA+P+A Sbjct: 669 AWGKKERTDKESPFQALPDA 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: 1666 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