Align Carbon starvation protein A (characterized, see rationale)
to candidate PP_4641 PP_4641 putative transporter
Query= uniprot:A0A0N9VZ52 (685 letters) >FitnessBrowser__Putida:PP_4641 Length = 688 Score = 1214 bits (3140), Expect = 0.0 Identities = 606/682 (88%), Positives = 642/682 (94%) Query: 4 LAKHLAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQL 63 L +H+ W A+AV+GA AL VVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIA KVMQL Sbjct: 7 LLRHIPWLALAVIGACALGVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIATKVMQL 66 Query: 64 DPGRATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG 123 DP RATPAV+NNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG Sbjct: 67 DPRRATPAVLNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAG 126 Query: 124 VVLAGAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVV 183 VVLAGAVQDFMVLF+STRRNGRSLGDMVREEMGR+PGTIALFGCFLIMIIILAVLALIVV Sbjct: 127 VVLAGAVQDFMVLFLSTRRNGRSLGDMVREEMGRIPGTIALFGCFLIMIIILAVLALIVV 186 Query: 184 KALADSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADP 243 KALA+SPWGMFTVMATIPIAMFMG+YMRYIRPGRIGEISVVGV+LLL SIWLGG IAADP Sbjct: 187 KALAESPWGMFTVMATIPIAMFMGIYMRYIRPGRIGEISVVGVVLLLASIWLGGVIAADP 246 Query: 244 VWAKAFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMP 303 VW AF+FTG+QITWML+GYGFVAAV+PVWL+LAPRDYLSTFLKIGTI+ LAIGILI P Sbjct: 247 VWGPAFTFTGVQITWMLVGYGFVAAVLPVWLVLAPRDYLSTFLKIGTILGLAIGILIIAP 306 Query: 304 ELKMPALTQFIDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYI 363 ELKMPALTQF DGTGPVWKG LFPFLFITIACGAVSGFHALI+SGTTPKLL +E +ARYI Sbjct: 307 ELKMPALTQFTDGTGPVWKGTLFPFLFITIACGAVSGFHALISSGTTPKLLDNETNARYI 366 Query: 364 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTVSSWGFMITPEAL 423 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAA+VG DV VAQTVSSWGF+ITPE L Sbjct: 367 GYGGMLMESFVAIMAMVAASVIEPGVYFAMNSPAAVVGTDVASVAQTVSSWGFLITPEQL 426 Query: 424 QAVAKDIGETTVLARAGGAPTLAVGIAQILHSVLPGENTMAFWYHFAILFEALFILTAVD 483 +AVA+DIGE T+LARAGGAPTLAVGIAQILH VLPGENTMAFWYHFAILFEALFILTAVD Sbjct: 427 EAVARDIGEHTILARAGGAPTLAVGIAQILHQVLPGENTMAFWYHFAILFEALFILTAVD 486 Query: 484 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLW 543 AGTRAGRFMLQDLLGSFVPALKRTESW ANL+ATAGCVA+WGYLLYQGVIDPLGGINTLW Sbjct: 487 AGTRAGRFMLQDLLGSFVPALKRTESWGANLLATAGCVALWGYLLYQGVIDPLGGINTLW 546 Query: 544 PLFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAI 603 PLFGISNQMLAGIALML TVVLIKMKRQRYIWVTLLPA WLLICTT AG IKLFD NPA+ Sbjct: 547 PLFGISNQMLAGIALMLGTVVLIKMKRQRYIWVTLLPAVWLLICTTAAGLIKLFDPNPAV 606 Query: 604 GFLSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVG 663 GFL+LAKKYS AL GQ+LAPAKDI QMQHVI+NAYTNA LT LFL VVFSILF+AIKVG Sbjct: 607 GFLALAKKYSTALDAGQVLAPAKDIGQMQHVIFNAYTNAGLTILFLLVVFSILFFAIKVG 666 Query: 664 ISAWGSKERTDKESPFQAIPEA 685 +A G KER+DKE+PFQA+P+A Sbjct: 667 YAALGRKERSDKETPFQALPDA 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: 1632 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: 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