Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 361 bits (927), Expect = e-104 Identities = 192/489 (39%), Positives = 299/489 (61%), Gaps = 4/489 (0%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 ++ + K FPGV ALDN F L GE+ AL+GENGAGKSTL+K L+GVY D G I L Sbjct: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR-FGL-LRRKEMEKRA 126 +G+ + AQ LGIG ++QE+NL+ ++S A N+FIGREP++ GL + E+ ++A Sbjct: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186 + A +D P+ +VA QQ+V I +A+ ++VLI+DEPTA+L+ E+ LF Sbjct: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL 246 ++R L+ +GV +++++H +D++ Q++DR++V+R+G ++ E ++ MM+GR L Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 Query: 247 DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306 D QR + V + + I +R GEI+G AGL+G+GRTE A I Sbjct: 262 DGE--QRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAI 319 Query: 307 FGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQ 366 FG P ++G +I G ++SP A GIG+ EDRK G+ V+ NI L+ + Sbjct: 320 FGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGR 379 Query: 367 RGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLIL 426 + + ++ +E A+ ++RQL I+TPS EQ LSGGNQQK+++++WLL L Sbjct: 380 FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFF 439 Query: 427 DEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPL 486 DEPTRGIDVGA +EI +L++ L G A+++ISSEL E++ + RV++M + + E+ Sbjct: 440 DEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELAR 499 Query: 487 AELSVPAIM 495 A+ + IM Sbjct: 500 ADATQEKIM 508 Score = 111 bits (278), Expect = 5e-29 Identities = 78/242 (32%), Positives = 127/242 (52%), Gaps = 10/242 (4%) Query: 260 SDKPVAAFKNYGKK--GTIA--PFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSG 315 S PV A +N K+ G +A E+ GE+ L G G+G++ +++ G+ DSG Sbjct: 18 SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77 Query: 316 TALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISR 375 L+ GKP + P QA LGIG ++ ++AA +NI + + ++ I Sbjct: 78 DILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAA---QNIFIGREPRKAMGLFIDE 134 Query: 376 KE-QQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGID 434 E ++ A F R PST P+ L+ QQ V +++ L + LI+DEPT ++ Sbjct: 135 DELNRQAAAIFARMRLDMDPST--PVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192 Query: 435 VGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAI 494 AE+ R+I L A G+ ++ IS +++EL ADRV +MRD K +A +P+ E S+ I Sbjct: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252 Query: 495 MN 496 ++ Sbjct: 253 IS 254 Score = 78.2 bits (191), Expect = 7e-19 Identities = 58/249 (23%), Positives = 116/249 (46%), Gaps = 10/249 (4%) Query: 3 TDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHAD 62 T ++ +L GL++ +A+ +V F+LR+GEI+ G GAG++ + +A+ G + Sbjct: 271 TSRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLE 326 Query: 63 RGTIWLEGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPK--RFGLL 117 G I + G K+ A A GIG + ++ L M V N+ + + R G + Sbjct: 327 AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFM 386 Query: 118 RRKEMEKRATELMASYGFSL-DVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASL 176 ++ + + A + V + S QQ + I + + +L DEPT + Sbjct: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGI 446 Query: 177 DTQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIE 236 D ++ L+ L ++G +++ ++ L +V ++S R+ V+ G G + Q + Sbjct: 447 DVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEK 506 Query: 237 LVKMMLGRE 245 ++++ RE Sbjct: 507 IMQLATQRE 515 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: 568 Number of extensions: 25 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: 520 Length adjustment: 34 Effective length of query: 466 Effective length of database: 486 Effective search space: 226476 Effective search space used: 226476 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