Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__Marino:GFF960 Length = 372 Score = 125 bits (315), Expect = 2e-33 Identities = 76/236 (32%), Positives = 134/236 (56%), Gaps = 9/236 (3%) Query: 4 NTEKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP 63 NT + EVLL R I+K+F G +AV+NV L I+KGE+ AL+G +G+GKSTL+++LAG Sbjct: 6 NTSAQAEVLLSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFET 65 Query: 64 DYEGQIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEY 123 G I L+G++V P N ++ Q L P+++ +NI + + + Sbjct: 66 PNAGSIMLDGQDVTALPPFLRPTN---MMFQSYALFPHMTVEQNIAMGLKQ----DKLPK 118 Query: 124 QKMFEQASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKR 183 ++ ++ + + + + + K + LS QQQ VA+A++L+ K++++DEP A+ K+ Sbjct: 119 SEIRDRVAAMLKLVKMEPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKK 178 Query: 184 -ETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEG-PIEEFD 237 TE ++ L+N G + + ++H EE +A R+ +M GR G PI+ ++ Sbjct: 179 LRTEMQLELVEILENVGATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYE 234 Score = 79.7 bits (195), Expect = 2e-19 Identities = 62/214 (28%), Positives = 106/214 (49%), Gaps = 23/214 (10%) Query: 281 LLVDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDA 340 L VD+V+ + KGE+ + G G+G++ LL + G G + + G+++ P Sbjct: 28 LAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNA-GSIMLDGQDVTALPPFLR 86 Query: 341 VKNGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEK- 399 N + ++ L M+V NI + GL +L K +R + Sbjct: 87 PTNMMF------QSYALFPHMTVEQNIAM------------GLKQDKLPKSEIRDRVAAM 128 Query: 400 LNIKTPSPY--QIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEI-YKLI 456 L + PY + + LSGG QQ+V LA+ LA +PK+LLLDEP +D ++E+ +L+ Sbjct: 129 LKLVKMEPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELV 188 Query: 457 SEMAVSGMGVVMVSSELPEILAMSDRILVMSEGR 490 + G +MV+ + E + M+ RI +M++GR Sbjct: 189 EILENVGATCLMVTHDQEEAMTMASRIAIMAQGR 222 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: 371 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 523 Length of database: 372 Length adjustment: 32 Effective length of query: 491 Effective length of database: 340 Effective search space: 166940 Effective search space used: 166940 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: 51 (24.3 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