Align FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate HSERO_RS05555 HSERO_RS05555 ABC transporter permease
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__HerbieS:HSERO_RS05555 Length = 618 Score = 180 bits (457), Expect = 1e-49 Identities = 128/428 (29%), Positives = 215/428 (50%), Gaps = 16/428 (3%) Query: 2 NWQLAAWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFS 61 NW L + L V + LG+P+A+ F V A++ S L + ++S Sbjct: 197 NWNLVVFFGLV-LAVSVLLGIPIAFCFGLATV--AFMLTVTTSPLAVVAGRFDEGMSSLI 253 Query: 62 LTPIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATT 121 L +PLFIL+G L+ TG+A+ +D + ++ + G L + + A S ISG+ A Sbjct: 254 LLAVPLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADM 313 Query: 122 AMLGSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGV 181 A + ++LP M RG + + A G + IPPS + + +GS+AG+SI+ L GG+ Sbjct: 314 AAVAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGI 373 Query: 182 LPGLLLAISFVAYIV--ASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVA 239 +PG++LA+ +A + SA++ VVLR ++ LP L+ + I Sbjct: 374 MPGIVLAV-LLAILARWRSAEIMEGIQRAPGRVVLR-------TLIIALPALLLPILIRT 425 Query: 240 VISGGVATPTEAAAIGCA-ATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTF 298 + GVAT TE + IG A + +A L+YR W+ L L T A+SG ILFII AT Sbjct: 426 AVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGM 485 Query: 299 SQVLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVK 358 S L+ SG ++ + + + S G + + +A I LG ++ + M+L P P+ K Sbjct: 486 SWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAK 545 Query: 359 SLGIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTM 418 ++G+ ++ + ++ ++ M +GL PP G+ Y + H + PY+G Sbjct: 546 AIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDV--AVKRIWPYLGALVVG 603 Query: 419 LILIFFWP 426 L+++ F P Sbjct: 604 LLIVAFVP 611 Lambda K H 0.329 0.143 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: 608 Number of extensions: 32 Number of successful extensions: 2 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: 439 Length of database: 618 Length adjustment: 35 Effective length of query: 404 Effective length of database: 583 Effective search space: 235532 Effective search space used: 235532 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 (21.8 bits) S2: 52 (24.6 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