Align ABC transporter for Lactose, ATPase component (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__psRCH2:GFF4209 Length = 383 Score = 221 bits (562), Expect = 3e-62 Identities = 130/344 (37%), Positives = 192/344 (55%), Gaps = 20/344 (5%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 L++ V K + + V L I GE +G SG GKSTLLRM+AG E + G + +D Sbjct: 23 LKIDRVTKKFDETVAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIFLD 82 Query: 64 DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123 + D+ P +R I M+FQSYAL+PHMTV +N+ F L+ G+P+AEIE+RV E ++++ Sbjct: 83 GQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLGLVQM 142 Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183 RKP QLSGGQRQRVA+ R++ + PK+ L DEP+ LD +LR M++E+ ++ +++ Sbjct: 143 TQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQIIERV 202 Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243 T V VTHDQ EAMT+A++I +M G + QVGSP+D+Y+ PA+ V FIG+ +N Sbjct: 203 GVTCVMVTHDQEEAMTMAERIAIMHLGWIAQVGSPMDIYETPASRLVCEFIGN--VNLFD 260 Query: 244 G-VIEIDEDQAYARLPDYGDAKIPVTLQAAAGT-----AVTIGIRPE---------HFDE 288 G +IE D A P + P+ + T +T IRPE + Sbjct: 261 GELIEDMGDHAVIASPGLEN---PIYVGHGISTRAEDKQITYAIRPEKLLIGTELPELER 317 Query: 289 AGPAALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLK 332 G + + +LGG + Y + G L R +K Sbjct: 318 PGYNWAKGVVHDIAYLGGHSVYYIKLPSGGVLQAFMANTERHVK 361 Lambda K H 0.321 0.139 0.396 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: 343 Number of extensions: 14 Number of successful extensions: 1 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: 358 Length of database: 383 Length adjustment: 30 Effective length of query: 328 Effective length of database: 353 Effective search space: 115784 Effective search space used: 115784 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: 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