Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 231 bits (588), Expect = 3e-65 Identities = 138/356 (38%), Positives = 196/356 (55%), Gaps = 32/356 (8%) Query: 4 LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63 + + K FG+ A+ + LT+ +GEF +GPSGCGK+TLLR++AG E G +++D Sbjct: 15 ITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILID 74 Query: 64 GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNL 123 G+DI++ P +KR + MVFQSYA++PHM+V +N+++ LK+ V K + +V A ++ L Sbjct: 75 GQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQL 134 Query: 124 TQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDL 183 R P +LSGGQRQRVA+ RA+V+ P+V L DEPLS LDA LR Q R E+ L + Sbjct: 135 GGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKV 194 Query: 184 GATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIG-------- 235 G T I VTHDQ EA+ LA R V+ G+++QV TP +LY+ P ++FVA FIG Sbjct: 195 GITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQVNLFEGV 254 Query: 236 ----TPQMNVVPVDKLPQPV-QQQAPAAPAGAAVGAIGLRPENITVR------------- 277 P V+ LP + P G V A +RPE I + Sbjct: 255 LAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGGTVWA-AIRPEKIELHKKADDTPPNLGDA 313 Query: 278 TTGATPVGGQVDLIEALGAETLIYVTTPGGAQF-VSRQN----DRTDLRVGDAVSL 328 G V G + LG + V GG + V R N D+ D ++G+ V L Sbjct: 314 PKGTNAVEGVIKHEAYLGGSSTYEVEIAGGRRVKVQRSNLTRWDQEDFKLGETVWL 369 Lambda K H 0.320 0.137 0.388 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: 333 Number of extensions: 10 Number of successful extensions: 1 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: 350 Length of database: 381 Length adjustment: 30 Effective length of query: 320 Effective length of database: 351 Effective search space: 112320 Effective search space used: 112320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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