Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Length = 526 Score = 464 bits (1194), Expect = e-135 Identities = 238/501 (47%), Positives = 344/501 (68%), Gaps = 4/501 (0%) Query: 4 STTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIY 63 + TP YLLE+ ++K FPGV AL +V L+VRP S+ ALMGENGAGKSTL+K + GIY Sbjct: 23 TATPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIY 82 Query: 64 QKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVD 122 Q D+G + +GK + F + AL+ GI+M+HQELNL+ S+ +N+W+GR G+ +D Sbjct: 83 QPDAGELRLRGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMID 142 Query: 123 QDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTE 182 +M+R T + + L I++DP VG LS+++ QM+EIAKA SY++ I+IMDEPTS++T+ Sbjct: 143 HREMHRCTAKLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITD 202 Query: 183 KEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKII 242 KEV HLF+II LK +G GI+YI+HKM E+F + DEV V RDG +I + + D +I Sbjct: 203 KEVAHLFSIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLI 262 Query: 243 AMMVGRSLNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKR 302 +MMVGR L+Q FP +E G+++L VR+L +DVSFDLH GEILGIAGL+G+ R Sbjct: 263 SMMVGRELSQLFPVREKPIGDLLLSVRDLK--LDGIFKDVSFDLHAGEILGIAGLMGSGR 320 Query: 303 TDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNS 362 T++ E +FGI G I L G+ + + + AI GFAL+TE+R+ +G++ L + N Sbjct: 321 TNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 380 Query: 363 LISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLL 422 ++ + +Y G + +++ + + +RVKTP I +LSGGNQQK ++ RWL+ Sbjct: 381 EMAVLPHYVGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 439 Query: 423 TQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG 482 T P IL+LDEPTRGIDVGAK EIY+LI+ LA +G +I+ISSE+PE+LG++DR++VM G Sbjct: 440 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 499 Query: 483 LVSGIVDTKTTTQNEILRLAS 503 + G +D TQ +++LAS Sbjct: 500 DLMGTLDRSEATQERVMQLAS 520 Score = 71.6 bits (174), Expect = 6e-17 Identities = 50/225 (22%), Positives = 103/225 (45%), Gaps = 6/225 (2%) Query: 31 NVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGI 90 +V+ + I + G G+G++ + + +FGI D G I G+ + A+E G Sbjct: 299 DVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGF 358 Query: 91 SMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVDQDKMYRETKAIFDELDIDIDPRA 145 +++ ++ L SV++NM + P F+ Q + + + +L + Sbjct: 359 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLE 418 Query: 146 R-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVY 204 + + TLS Q +A+ N +I+I+DEPT + ++ +I L G ++ Sbjct: 419 QCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIM 478 Query: 205 ISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249 IS ++ E+ + D V V+ +G + T + T ++++ + G S Sbjct: 479 ISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMS 523 Lambda K H 0.318 0.136 0.384 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: 653 Number of extensions: 28 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: 506 Length of database: 526 Length adjustment: 35 Effective length of query: 471 Effective length of database: 491 Effective search space: 231261 Effective search space used: 231261 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 Apr 09 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