Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_008409656.1 DESHY_RS00685 ABC transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >NCBI__GCF_000315365.1:WP_008409656.1 Length = 509 Score = 307 bits (787), Expect = 5e-88 Identities = 171/496 (34%), Positives = 290/496 (58%), Gaps = 5/496 (1%) Query: 10 EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQI 69 + L+E + I+K FPGV+A + + LQ+ +GEV AL+GENG+GKSTLM IL+G+Y G+I Sbjct: 4 DFLVEMKQISKRFPGVLANDCIDLQVKRGEVLALLGENGSGKSTLMSILSGLYRPDAGEI 63 Query: 70 FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129 ++EG++V F++PR+A + GI ++ Q V S AENI L + + +++ K ++ Sbjct: 64 YIEGRKVNFKSPRDAIDAGIGMVHQHFKQVDTFSVAENIILGSK--EKKCLLQAGKAEKE 121 Query: 130 ASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLF 189 +++ G+ ++P K+ LS +++Q V I K L +K++I+DEPT+ + +E +LF Sbjct: 122 IAEISRGYGLQVEPTAKIWQLSIAERQRVEIVKMLYRGSKVLILDEPTAVLTPQEARELF 181 Query: 190 NIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRS 249 +IR + G+S+I I+H+L E+ E+ADRV ++R GR V ++ + +L RLM+G+ Sbjct: 182 QVIRQMTARGQSIILITHKLNEVMEVADRVTILRGGRAVATRERKQVNQRELARLMMGQD 241 Query: 250 IDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTEL 309 + K+ +EI R++ S D ++ + D++ VR+GE+LGI G+ G GR EL Sbjct: 242 VVVPSQKQPGQFGEEILRLDRASAAS-DSRRPGLQDITLTVRQGEILGIAGIAGNGRREL 300 Query: 310 LEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITL 369 E I G P GK++I GK++ SP + ++ G+ +PEDR GL+ + + N+ L Sbjct: 301 AEVIAGLRP-LDGGKIYICGKDVTNLSPMEIIQEGVSYIPEDRLGTGLVPNLGAVDNLIL 359 Query: 370 PSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLA 429 + R I + + I ++ +K V+ LSGGN Q+++LA+ LA Sbjct: 360 KEYRRPWLSRG-PFICRRKAAQFATRLIHEVGVKVTGLDAPVKKLSGGNLQRLLLARELA 418 Query: 430 IKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEG 489 PKV++ P RG+D+ A ++K++ E G +V++S +L E+L +SD I V+ +G Sbjct: 419 SSPKVIVAVYPVRGLDIAASEAVHKMLLEQRSKGAAIVLISEDLEELLKLSDNIGVLYKG 478 Query: 490 RKTAEFLREEVTEEDL 505 EE E + Sbjct: 479 SLMGVLPVEEAEPEKI 494 Score = 103 bits (256), Expect = 2e-26 Identities = 67/238 (28%), Positives = 125/238 (52%), Gaps = 11/238 (4%) Query: 284 DDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKN 343 D + V++GEVL + G G+G++ L+ + G + G+++I G+++ SPRDA+ Sbjct: 23 DCIDLQVKRGEVLALLGENGSGKSTLMSILSGLYRPDA-GEIYIEGRKVNFKSPRDAIDA 81 Query: 344 GIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIK 403 GIG+V + K SV NI L S K +++ + EKEI I + Sbjct: 82 GIGMVHQHFKQVDTF---SVAENIILGSKEKKCLLQA-----GKAEKEIAE--ISRGYGL 131 Query: 404 TPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSG 463 P + LS +Q+V + K L KVL+LDEPT + E++++I +M G Sbjct: 132 QVEPTAKIWQLSIAERQRVEIVKMLYRGSKVLILDEPTAVLTPQEARELFQVIRQMTARG 191 Query: 464 MGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVETTQR 521 +++++ +L E++ ++DR+ ++ GR A R++V + +L + + + V V + ++ Sbjct: 192 QSIILITHKLNEVMEVADRVTILRGGRAVATRERKQVNQRELARLMMGQDVVVPSQKQ 249 Score = 102 bits (255), Expect = 3e-26 Identities = 63/227 (27%), Positives = 126/227 (55%), Gaps = 7/227 (3%) Query: 28 VNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLEGKEVRFRNPREAQEN 87 + ++TL + +GE+ + G G G+ L +++AG+ P G+I++ GK+V +P E + Sbjct: 274 LQDITLTVRQGEILGIAGIAGNGRRELAEVIAGLRPLDGGKIYICGKDVTNLSPMEIIQE 333 Query: 88 GIALIPQE---LDLVPNLSSAENIFLS--REPVNEFG-VIEYQKMFEQASKLFSKLGVNI 141 G++ IP++ LVPNL + +N+ L R P G I +K + A++L ++GV + Sbjct: 334 GVSYIPEDRLGTGLVPNLGAVDNLILKEYRRPWLSRGPFICRRKAAQFATRLIHEVGVKV 393 Query: 142 DP-KTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNIIRSLKNEGK 200 V+ LS Q + +A+ L+ K+I+ P + +E + ++ +++G Sbjct: 394 TGLDAPVKKLSGGNLQRLLLARELASSPKVIVAVYPVRGLDIAASEAVHKMLLEQRSKGA 453 Query: 201 SVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVG 247 +++ IS LEE+ +++D + V+ G +G P+EE + +K+ +M+G Sbjct: 454 AIVLISEDLEELLKLSDNIGVLYKGSLMGVLPVEEAEPEKIGLMMLG 500 Lambda K H 0.317 0.137 0.372 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: 593 Number of extensions: 38 Number of successful extensions: 10 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: 523 Length of database: 509 Length adjustment: 35 Effective length of query: 488 Effective length of database: 474 Effective search space: 231312 Effective search space used: 231312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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