Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_090443905.1 BLS63_RS11175 iron ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >NCBI__GCF_900100495.1:WP_090443905.1 Length = 538 Score = 51.6 bits (122), Expect = 4e-11 Identities = 55/183 (30%), Positives = 86/183 (46%), Gaps = 13/183 (7%) Query: 75 LLSALVGSLN-GYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSIG---LYGS 130 L+ VG N GY L GS L A++L + + ++IPL ++ G L GS Sbjct: 355 LMRGAVGLANLGYALP-----GSMLAVAIMLAFSQLD-RHLVIPLSGWLGGAGKPLLLGS 408 Query: 131 LFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVV 190 L L+L ++I + + N + I L EAAR G G G+F V LPL VP + Sbjct: 409 LSALLLAYLIRFMAVAYGPLENSLARIRPSLPEAARSLGVGGIGLFFKVYLPLLVPGALA 468 Query: 191 VAIWQFTQIWNEFLFAVTLTRPES-QPITVALAQLAG-GEAVKWNLPMAGAILAALPTLL 248 A+ F + E + A L RP ++V + ++ GE + +LP +L L ++ Sbjct: 469 AALLVFVDVLKE-MPATLLMRPFGWDTLSVRVFEMTSEGEWARASLPALTLVLVGLLPVI 527 Query: 249 VYI 251 + I Sbjct: 528 LLI 530 Score = 41.6 bits (96), Expect = 4e-08 Identities = 57/219 (26%), Positives = 87/219 (39%), Gaps = 51/219 (23%) Query: 92 PFRGSGLLFALILFGMFI---PYQSILIPLFQFMKSIGLYGSLFGLVLVHVIYGIPIVTL 148 PF + A + G+ P QS+L F + S G+++V V+ P V L Sbjct: 94 PFAIPAYVLAFVFVGLLDFAGPLQSLLREWFGTGVRLPRVRSTGGVIIVLVLVFYPYVYL 153 Query: 149 IFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPA---------------FVVVAI 193 + RN + L+EAAR+ G + F V LP++ PA F V++ Sbjct: 154 LARNAFLAQGKGLMEAARVLGLSPWQAFWRVALPMARPAIGAGLALAVMETLADFGAVSV 213 Query: 194 WQF--------------------TQIWNEFLFAVTL-----------TRPESQ-PITVAL 221 + F TQ+ + LFAV L RP ++ P AL Sbjct: 214 FNFDTFTTAIYKTWYSFYSLTSATQLASLLLFAVMLALYGERRARGAVRPSNERPRGKAL 273 Query: 222 AQLAGGEAVKWNLPMAGAILAALPTLLVYILLGRYFLRG 260 L GG+A+ + G + A + V LLG ++ RG Sbjct: 274 YHLKGGKALAAS-AWCGLVFACAFVIPVLQLLGWFWQRG 311 Lambda K H 0.330 0.146 0.461 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: 442 Number of extensions: 22 Number of successful extensions: 3 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: 268 Length of database: 538 Length adjustment: 30 Effective length of query: 238 Effective length of database: 508 Effective search space: 120904 Effective search space used: 120904 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 (21.8 bits) S2: 50 (23.9 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