Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_005454736.1 SACCYDRAFT_RS06670 ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >NCBI__GCF_000244975.1:WP_005454736.1 Length = 338 Score = 140 bits (352), Expect = 6e-38 Identities = 100/320 (31%), Positives = 163/320 (50%), Gaps = 20/320 (6%) Query: 1 MIARRFIPLWITASLLL--TMFLVGT---FQFDGFASGRVVTNLLRDNAFLLITALGMTL 55 M+ R L ASL++ F + + F +D F T +L + A+G T Sbjct: 23 MLKSRLQQLLAFASLIVIYAFFSIASPYFFTYDNF------TAILFSTVVIGTLAIGTTF 76 Query: 56 VIISGGIDLSVGAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKL 115 VII+GGIDLS+G +AL V++ + + + L + + G L G + G I K+ Sbjct: 77 VIITGGIDLSIGTGMALCAVMSGVFLVDLGLPLPLGVLCAVLFGGLVGLVNGLNIAFLKI 136 Query: 116 QPFIVTLAGMFLARGLATTLSEESIAI--DHPFYDAVAEMSIALPGNGALDLSSLIFILF 173 PFI TLA M +A GLA LS+ + D P Y ++ ++ +PG +D + + IL Sbjct: 137 PPFIATLAMMLVAEGLALVLSDSAPIYFNDVPGYVELSRGNL-IPG---VDFPNAVLILI 192 Query: 174 FVIIAVVMHYTR--FGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTF 231 V I + TR G Y+IG N+ + L GI + + I++YA + LAG++ + Sbjct: 193 AVAIIASVLLTRSVLGRYTYSIGSNEEATALSGIDVRRWKIAVYAFAGLFIGLAGVLISA 252 Query: 232 YTFSGYALGAIGVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSS 291 S +G EL AIAAVVIGGT L+GG G +LGT++G +++ V+ + S+ Sbjct: 253 RLGSAQPATGMGYELQAIAAVVIGGTSLSGGKGSILGTLIGALIISVLNNGLQI-MSIPQ 311 Query: 292 WWTKIVIGLLLFFFILLQKL 311 W +++G ++ + ++ Sbjct: 312 EWQNVILGCVILVAVYADRM 331 Lambda K H 0.330 0.145 0.424 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: 363 Number of extensions: 26 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: 320 Length of database: 338 Length adjustment: 28 Effective length of query: 292 Effective length of database: 310 Effective search space: 90520 Effective search space used: 90520 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 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