Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Phaeo:GFF2651 Length = 522 Score = 266 bits (679), Expect = 2e-75 Identities = 165/475 (34%), Positives = 257/475 (54%), Gaps = 10/475 (2%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +LR + ++K F V A D+V F L GE++ALLGENGAGK+TL+ L G Y AD G + L Sbjct: 15 VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128 G + P A G+G V+Q L N++V +N+ +G EP LR + R Sbjct: 75 FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPAKARIRA 134 Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188 L + +D ++R +V +Q V I +A+ A++LILDEPTA L QE + LF + Sbjct: 135 LAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATL 194 Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL-- 246 R+ +RG+S+IF++H L +V +SDR+ VLR+G V R+T + L +M+G ++ Sbjct: 195 REAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADVVP 254 Query: 247 DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306 A G LL + V + G + L++ G+I GLAG+ G+G+ ++++ Sbjct: 255 AKFAANTPGPALLQLRDVTT-PSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLV 313 Query: 307 FGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA- 365 G+ SG+ + G SP +A GI PEDR G IA + EN IL A Sbjct: 314 SGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETYAT 373 Query: 366 ---QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQ 422 RGWL + ++ A+ I +R P + I LSGGN QK++L R L PQ Sbjct: 374 RFSHRGWL---DWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQ 430 Query: 423 FLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD 477 ++ ++P RG+D+GA + + CA G A+L+IS +L+E++ +D + ++ + Sbjct: 431 IILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISE 485 Score = 72.8 bits (177), Expect = 3e-17 Identities = 66/238 (27%), Positives = 117/238 (49%), Gaps = 14/238 (5%) Query: 263 PVAAFKNYGKK-GTIAPFD---LEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTAL 318 PV +N K+ G++ D ++ PGE++ L G G+G+T ++FG AD+G Sbjct: 14 PVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73 Query: 319 IKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGW-LRPISRKE 377 + G P +P A G+G + + +V ENI L ++ G LR K Sbjct: 74 LFGAPLPPGAPRAALDGGVGMVHQHFT---LADNLTVWENITLGVEPLLGLGLRAGPAKA 130 Query: 378 Q-QEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVG 436 + + +AE+F ++ P+ + + L+ G +Q+V + + L + LILDEPT + Sbjct: 131 RIRALAEQFHLKVD---PNAK--VSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQ 185 Query: 437 AHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAI 494 + + GL+++ IS +L E++ +DRV+++R K VAE A+ A+ Sbjct: 186 ESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDAL 243 Score = 59.3 bits (142), Expect = 3e-13 Identities = 55/236 (23%), Positives = 104/236 (44%), Gaps = 17/236 (7%) Query: 25 LDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQL 84 L +V L G+I L G +G G++ L ++G+ G++ L G A + + A Sbjct: 283 LRHVSLDLAAGQITGLAGVSGNGQAALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITA 342 Query: 85 GIGTVYQE---VNLLPNMSVADNLFIGREPKRF---GLLRRKEMEKRATELMASYGFSLD 138 GI + ++ + + + +N + RF G L + A ++ Y D Sbjct: 343 GIARIPEDRHKTGTIADFDLTENAILETYATRFSHRGWLDWRAARDFAKTVITGY----D 398 Query: 139 VREP-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRD 193 VR P + S Q + + R ++ S ++++ ++P LD V + + + + Sbjct: 399 VRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQIILANQPVRGLDIGAVTYVHEQLAKACA 458 Query: 194 RGVSLIFVTHFLDQVYQVSDRITVLRNGSF-VGCRETCELPQIELVKMMLGRELDT 248 RG +++ ++ LD++ Q+SD I V+ G G + P+ EL M G DT Sbjct: 459 RGAAVLLISEDLDEIMQLSDVIHVISEGRLSPGFARGSKQPE-ELGAWMAGHGFDT 513 Lambda K H 0.321 0.138 0.391 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: 554 Number of extensions: 29 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 500 Length of database: 522 Length adjustment: 35 Effective length of query: 465 Effective length of database: 487 Effective search space: 226455 Effective search space used: 226455 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: 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