Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 290 bits (742), Expect = 8e-83 Identities = 181/480 (37%), Positives = 269/480 (56%), Gaps = 13/480 (2%) Query: 13 PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72 PV+ +V++ FG L DV + PGE HAL+G NGAGKST + IL G P GEV Sbjct: 4 PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVL 63 Query: 73 FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132 G + R+A V ++Q + L+V EN+F+ R+ RG +D +AM+ ++R Sbjct: 64 LDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAESR 123 Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192 LL+ V AR LSV RQ+VEIA+AL AR +I+DEPTA L E L + Sbjct: 124 RLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQ 183 Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG-ERG 251 + L+ G L+ SH L EV I VTVLRD R +++AP L +++ E M G E Sbjct: 184 VDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243 Query: 252 GLAVADAAARGALPADTAVALELKELTGADY-EGVSFTVKRGEVVGLTGATSSGRTSVAE 310 GL ++ PA V LE+ LT + SFT++RGEV+G G SGRT + E Sbjct: 244 GLFPPKSS-----PAPEPV-LEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELME 297 Query: 311 AIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIA 370 I GLR A G + ++G+ LP V A+ A G+ + +DR +GL+L + + EN ++ Sbjct: 298 GIVGLRPA-TGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLAL 356 Query: 371 RVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSG-LSGGNQQKVVMARALATNPNV 429 G+ I A++ A Q + D + G + +G LSGGNQQK+++A+ + P V Sbjct: 357 DRFGRVLIDKAAEERALTQAISDF--DIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRV 414 Query: 430 LVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAE 488 +++ +PT G+DV +K+ + + R+ EG++V+VVS EL + + +RV+VM GR+A E Sbjct: 415 VIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGE 474 Score = 63.5 bits (153), Expect = 2e-14 Identities = 60/226 (26%), Positives = 98/226 (43%), Gaps = 10/226 (4%) Query: 30 LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89 + D S + GE G G+G++ L+ + GLR P TGEVR G+ P + A Sbjct: 269 VRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLR-PATGEVRMEGSPLPHASVSAA--R 325 Query: 90 RVACVY-----QHSTIIRDLSVAENLFINRQPLRGGV-IDWQAMRRDARALLDHWKIDVR 143 VY + ++ + ENL + G V ID A R + + I V Sbjct: 326 AAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRVLIDKAAEERALTQAISDFDIRVG 385 Query: 144 EDA-RAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVT 202 + AG LS +Q + +A+ + R +I+DEPT +D ++++ I+ L EG + Sbjct: 386 DRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRS 445 Query: 203 FLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248 + +S L EV + V V+ R A+ E ++ G Sbjct: 446 VIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEAITEENIVRLAMG 491 Lambda K H 0.318 0.134 0.377 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: 563 Number of extensions: 31 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 510 Length of database: 499 Length adjustment: 34 Effective length of query: 476 Effective length of database: 465 Effective search space: 221340 Effective search space used: 221340 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 (21.7 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