Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate AZOBR_RS29435 AZOBR_RS29435 hemin ABC transporter permease
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__azobra:AZOBR_RS29435 Length = 369 Score = 171 bits (432), Expect = 3e-47 Identities = 113/336 (33%), Positives = 170/336 (50%), Gaps = 22/336 (6%) Query: 3 IALVIFITLALAGCALLSLHMGVIPVPWRALLTDWQA---------GHEHYYVLMEYRLP 53 + ++ + ALA L ++ G + VP L+ A + VL RL Sbjct: 26 VPVLAALAAALAVAVLTAVATGGVSVPLDRSLSHLAALLGLPGTPLSERDWMVLTMLRLA 85 Query: 54 RLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPS-------- 105 R++LA VG L VAGV +Q + RNPLA P ++GV+ A+LA A++L S Sbjct: 86 RIVLAAAVGVTLGVAGVALQAVFRNPLADPGLVGVSSGAALAGSAAMVLGVSGLGLARSG 145 Query: 106 -LPVMVLPLLAFAGGMAGLILLKMLAKT---HQPMKLALTGVALSACW-ASLTDYLMLSR 160 VLPL AF G +A +L+ +++ + P + L G+A++A A + + L Sbjct: 146 LSLATVLPLAAFLGALAATVLILAISRRDGRNSPATMLLAGIAVNAIGGAGIGLFSYLGD 205 Query: 161 PQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVS 220 + W+ G G W+ + A+ LM L L+ R LDL A+G+ A G+ Sbjct: 206 DLALRQMTFWMMGGFGGSSWAQIGPAMVLMGLATAGLLAGARRLDLFAMGEREAFLQGLD 265 Query: 221 VPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLL 280 +LL VA G I F+GL+VPH+MR + G HRRL+P +AL A+LL Sbjct: 266 PHRFAVRTVLLVALGVGAAVAVSGLIGFVGLIVPHVMRILLGPVHRRLMPATALAAAVLL 325 Query: 281 VVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316 V+AD +AR I P ++P G+L +G P+F+WLL R Sbjct: 326 VLADTVARTIAAPADVPAGLLLGAVGGPFFLWLLRR 361 Lambda K H 0.330 0.142 0.447 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: 306 Number of extensions: 11 Number of successful extensions: 2 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: 318 Length of database: 369 Length adjustment: 29 Effective length of query: 289 Effective length of database: 340 Effective search space: 98260 Effective search space used: 98260 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: 49 (23.5 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