Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_011841070.1 RSPH17029_RS07675 carbohydrate ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >NCBI__GCF_000015985.1:WP_011841070.1 Length = 373 Score = 493 bits (1270), Expect = e-144 Identities = 256/385 (66%), Positives = 309/385 (80%), Gaps = 12/385 (3%) Query: 1 MDNIAGSKSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAMFPSEQNL 60 MDNIAG++SSL WAV L+VV LV+LW LPT GL VSSFR +QI+++GWW A+FP+EQ + Sbjct: 1 MDNIAGTRSSLVWAVHLAVVALVLLWTLPTLGLLVSSFRDRDQIAATGWWAALFPAEQRM 60 Query: 61 TLRAADPDDFRMPQGDLFVVKGNLFEDEGISEAEISVWGTSSRDVAAYTAGETADLGDGE 120 +R A D+ R +GDL++V+G+L E E ++ +GTS+R A+ AGET +L +G Sbjct: 61 VVRLAGADEQRQ-EGDLWIVEGDLTE-----EGTLNRFGTSARAPFAHAAGETGELSNGG 114 Query: 121 TITVQSNGAYVWSGTDDQISGRGQRVFVTATTPPEFTFANYENMLLDPNNSEGMARAFFN 180 +TV+++G+Y RG R+FV T P FT ANYE +L +EG+ RAF N Sbjct: 115 RVTVEADGSYRAEAAQP-FGDRGPRLFVAVDTAPRFTTANYERVLF----AEGIGRAFLN 169 Query: 181 TLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNAI 240 T+TVTIPATIIPILVAAFAAYALAWMEFPGRALLIA +VGLLVVPLQLALIPLL LHNA+ Sbjct: 170 TMTVTIPATIIPILVAAFAAYALAWMEFPGRALLIAAVVGLLVVPLQLALIPLLQLHNAV 229 Query: 241 GIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSF 300 GIGK YLG WLAH+ FG+PLAIYLLRNYMVGLPR+IIE+A+VDGATDFQIF KI+LPLSF Sbjct: 230 GIGKDYLGIWLAHSAFGLPLAIYLLRNYMVGLPREIIESARVDGATDFQIFVKIILPLSF 289 Query: 301 PALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVS 360 PALASFAIFQFLWTWNDLLVA VFL + T + VMT + ELLG+RGG+WEILA +AFVS Sbjct: 290 PALASFAIFQFLWTWNDLLVATVFLSN-TPEQLVMTGVLRELLGSRGGDWEILAASAFVS 348 Query: 361 IAVPLLVFFSMQRFLVRGLLAGSVK 385 IAVP++VFF+MQR+LVRGLLAGSVK Sbjct: 349 IAVPIVVFFAMQRYLVRGLLAGSVK 373 Lambda K H 0.323 0.138 0.419 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: 483 Number of extensions: 19 Number of successful extensions: 6 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: 385 Length of database: 373 Length adjustment: 30 Effective length of query: 355 Effective length of database: 343 Effective search space: 121765 Effective search space used: 121765 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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