Align N-acetylglucosamine transporter nagP (characterized)
to candidate 6936761 Sama_0948 multiple antibiotic resistance (MarC)-related protein (RefSeq)
Query= reanno::ANA3:7025962 (432 letters) >FitnessBrowser__SB2B:6936761 Length = 441 Score = 437 bits (1124), Expect = e-127 Identities = 232/432 (53%), Positives = 304/432 (70%), Gaps = 11/432 (2%) Query: 8 QKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALP 67 ++SS LPM I+ LFFI GF TWLNGSL+P+LK I +LN FQA + F+FYIA T ALP Sbjct: 13 RRSSVLPMTIIGILFFIFGFVTWLNGSLIPFLKVICELNEFQALFVTFAFYIAYTVMALP 72 Query: 68 SAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNP 127 + ++R+ GY+NGMA+G+GIM++ L FIPAA + F LFL A ++GTG T+LQTA NP Sbjct: 73 MSSILRRTGYRNGMAIGLGIMVVGSLAFIPAAYSANFLLFLGALFILGTGLTILQTASNP 132 Query: 128 YVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALI---LDSFKDRIGTTLTQ----VQ 180 YVV +GP+ESAA R+S+MGI+NK AGV+ PL+F+AL+ L++F + + L+ VQ Sbjct: 133 YVVHIGPKESAAMRISIMGIINKLAGVVVPLLFTALVLSGLENFDEAHLSALSDADRAVQ 192 Query: 181 IDEMANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAF 240 I E+++ LV PY+ MA+ + L VK S LPEL E+ + +KG I P + Sbjct: 193 ITELSSRLVMPYIYMAVALLALIALVKFSGLPELEFEEAESAEGEKGSI---TQFPQVIL 249 Query: 241 GVIALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQP 300 G IALF YV +EVIAGDTIG + SLGV ++ +TSYTMV MV+GY +G++ IPRFISQ Sbjct: 250 GAIALFAYVGIEVIAGDTIGLYGQSLGVANFASLTSYTMVFMVIGYAIGVLCIPRFISQE 309 Query: 301 TALMISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPA 360 AL+ SAI G L L +FG S +A+AL G +P++++F+A +GLA+A+VWPA Sbjct: 310 RALLASAIAGGLCVLGAVFGSTESTTLASALWGWMGVPLVPNSVVFVAMMGLAHALVWPA 369 Query: 361 VWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFIL 420 VWPLAL GLGK T+ GSALLIMGI+GGA PL +G + + Q GY V LPCYLFIL Sbjct: 370 VWPLALDGLGKFTAQGSALLIMGISGGAILPLLFGKVAHFSGETQL-GYWVGLPCYLFIL 428 Query: 421 FYAVKGHKMRHW 432 FYAVKGHKMR W Sbjct: 429 FYAVKGHKMRSW 440 Lambda K H 0.327 0.141 0.421 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: 664 Number of extensions: 40 Number of successful extensions: 4 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: 432 Length of database: 441 Length adjustment: 32 Effective length of query: 400 Effective length of database: 409 Effective search space: 163600 Effective search space used: 163600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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