Align Carbon starvation protein A (characterized, see rationale)
to candidate WP_057509147.1 ABB28_RS13685 carbon starvation protein A
Query= uniprot:A0A0N9VZ52 (685 letters) >NCBI__GCF_001431535.1:WP_057509147.1 Length = 693 Score = 1074 bits (2778), Expect = 0.0 Identities = 526/676 (77%), Positives = 597/676 (88%), Gaps = 4/676 (0%) Query: 8 LAWFAVAVLGAFALSVVALRRGEAINALWIVVAAVAIYLVAYRYYSLFIANKVMQLDPGR 67 L W +A+LGAF L VALRRGE INALWIVVAAV+IYL+AYR+Y LF+A+KV+QLDP R Sbjct: 7 LGWALLALLGAFCLGTVALRRGEPINALWIVVAAVSIYLIAYRFYGLFVASKVLQLDPTR 66 Query: 68 ATPAVVNNDGLDYVPTNKHILFGHHFAAIAGAGPLVGPVLAAQMGYLPGTLWLIAGVVLA 127 ATPAV+NNDGLDYVPTNKH+LFGHHFAAIAGAGPLVGPVLAAQMGYLPG LWL+ GVVLA Sbjct: 67 ATPAVLNNDGLDYVPTNKHVLFGHHFAAIAGAGPLVGPVLAAQMGYLPGLLWLVVGVVLA 126 Query: 128 GAVQDFMVLFMSTRRNGRSLGDMVREEMGRVPGTIALFGCFLIMIIILAVLALIVVKALA 187 GAVQDFM+L +S+RRNGRSLGD+VREEMG VPGTIALFG FLIMIIILAVLA++VVKALA Sbjct: 127 GAVQDFMILVLSSRRNGRSLGDLVREEMGPVPGTIALFGAFLIMIIILAVLAMVVVKALA 186 Query: 188 DSPWGMFTVMATIPIAMFMGVYMRYIRPGRIGEISVVGVLLLLGSIWLGGQIAADPVWAK 247 +SPWGMFTV+AT+PIA+FMGVYMRYIRPG+IGEISVVG++LLLGSIW GG +AADPVW Sbjct: 187 ESPWGMFTVIATMPIAIFMGVYMRYIRPGKIGEISVVGLILLLGSIWFGGIVAADPVWGP 246 Query: 248 AFSFTGIQITWMLIGYGFVAAVMPVWLILAPRDYLSTFLKIGTIMALAIGILITMPELKM 307 AF+FT QITWMLIGYGFVA+V+PVWL+LAPRDYLSTFLKIGTI+ALA+GILI MPELKM Sbjct: 247 AFTFTAKQITWMLIGYGFVASVLPVWLLLAPRDYLSTFLKIGTIIALAVGILIVMPELKM 306 Query: 308 PALTQF-IDGTGPVWKGGLFPFLFITIACGAVSGFHALIASGTTPKLLASEGHARYIGYG 366 PALTQF G GPVWKGG+FPFLFITIACGAVSGFHALIASGTTPKLLA+E HARYIGYG Sbjct: 307 PALTQFAASGDGPVWKGGMFPFLFITIACGAVSGFHALIASGTTPKLLANEAHARYIGYG 366 Query: 367 GMLMESFVAIMAMVAASVIEPGVYFAMNSPAAIVGGDVVQVAQTV-SSWGFMITPEALQA 425 GMLMESFVA+MA+VAAS+IEPG+YFAMNSPA+++G D V A + ++WGF ITPE L+A Sbjct: 367 GMLMESFVAVMALVAASIIEPGIYFAMNSPASVIGADAVSAAHYITTNWGFTITPEQLEA 426 Query: 426 VAKDIGETTVLARAGGAPTLAVGIAQILHSVLP--GENTMAFWYHFAILFEALFILTAVD 483 A IGE T+L RAGGAPTLAVGIA ILH +P G+ MAFWYHFAILFEALFILTAVD Sbjct: 427 TAVAIGEPTILHRAGGAPTLAVGIAMILHEAIPSAGDAMMAFWYHFAILFEALFILTAVD 486 Query: 484 AGTRAGRFMLQDLLGSFVPALKRTESWTANLIATAGCVAMWGYLLYQGVIDPLGGINTLW 543 AGTRAGRFMLQDLLG+F+PALK+TESW+AN++ATAGCVA+WGYLLY GV+DP GGI TLW Sbjct: 487 AGTRAGRFMLQDLLGNFIPALKKTESWSANILATAGCVALWGYLLYSGVVDPFGGIQTLW 546 Query: 544 PLFGISNQMLAGIALMLSTVVLIKMKRQRYIWVTLLPAAWLLICTTTAGFIKLFDANPAI 603 PLFGISNQMLAGIALML TVVL KMKR RY WVT +PA WLLICTT AG IK+FD+NPA Sbjct: 547 PLFGISNQMLAGIALMLGTVVLFKMKRDRYAWVTAVPAVWLLICTTYAGLIKIFDSNPAQ 606 Query: 604 GFLSLAKKYSDALANGQILAPAKDITQMQHVIYNAYTNATLTALFLFVVFSILFYAIKVG 663 GFL+ A K+ DA+A+G I APAK + QMQ ++ NAY N TLT LFL VVFSILFYA+K Sbjct: 607 GFLAQAHKFQDAIASGTITAPAKTVGQMQQIVVNAYVNTTLTVLFLLVVFSILFYALKTI 666 Query: 664 ISAWGSKERTDKESPF 679 +A + +RTDKE+ + Sbjct: 667 AAARRTPQRTDKETEY 682 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: 1512 Number of extensions: 56 Number of successful extensions: 6 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: 693 Length adjustment: 39 Effective length of query: 646 Effective length of database: 654 Effective search space: 422484 Effective search space used: 422484 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 24 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