Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate SM_b21429 SM_b21429 iron ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__Smeli:SM_b21429 Length = 253 Score = 127 bits (318), Expect = 3e-34 Identities = 87/257 (33%), Positives = 139/257 (54%), Gaps = 15/257 (5%) Query: 1 MTLRTENLTVSYGTDKVLNDVSL-SLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTV 59 ++L +++ +YG VL+D++ +L G +TA+IGPN GKSTL + L Sbjct: 2 VSLALKDVGATYGRRVVLSDINTGTLKGGHLTAVIGPNAAGKSTLFKRIAGLAA------ 55 Query: 60 FLGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARV 119 G +++ + A + +PQ +TV E V S W ++ + A + Sbjct: 56 --GPGLVHLSDTANGAEAICYMPQDTGANAVLTVYESVLLSAKQG-SGW-KVKDGELAEI 111 Query: 120 NVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMR 179 + + +IN LA R L ELSGGQRQ +A L + V+L+DEPT+ LD+ Q++++ Sbjct: 112 DRVLAALKINDLAFRGLGELSGGQRQLVSIAQALVRKPEVLLMDEPTSALDLFRQIEVLG 171 Query: 180 LMGELRTQ-GKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVE 238 M L Q G V+ LHDLN A RYC+ +V++ G V+A G V+T +L++V+ VE Sbjct: 172 FMKRLAAQSGMAVLIALHDLNHALRYCEDTIVISGGSVVASGPTHTVVTADMLKSVYRVE 231 Query: 239 AEIHPEPVS-GRPMCLM 254 A + E S GRP+ ++ Sbjct: 232 ARV--EACSRGRPVIIV 246 Lambda K H 0.320 0.134 0.393 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: 161 Number of extensions: 9 Number of successful extensions: 3 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: 255 Length of database: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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