GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglF in Bacillus safensis FO-36b

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_034283552.1 BA81_RS15550 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000691165.1:WP_034283552.1
          Length = 632

 Score =  435 bits (1119), Expect = e-126
 Identities = 248/632 (39%), Positives = 369/632 (58%), Gaps = 17/632 (2%)

Query: 3   ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62
           +LA  I+  VGG +N+VS   CATRLR  LK  +    E +   PG+I VVE+GGQFQVV
Sbjct: 9   KLAEDILEAVGGEENVVSAARCATRLRLVLKRSNPKAKEAVNAMPGVITVVENGGQFQVV 68

Query: 63  IGNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGILK 122
           IG HV +V+   +S+  L + ++    N++KG +LNR +  +S +F P + ++AA GIL+
Sbjct: 69  IGQHVGEVYEHFSSLVQL-QPSEDDQVNENKGTVLNRVIATMSAVFAPFVYILAAAGILQ 127

Query: 123 GMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGALV 182
           G L L      +  ++GTY +    S A F F PI +  TA K F  N + A+    ALV
Sbjct: 128 GALILINLLFPSFSKTGTYEVFSFISWAPFTFLPIFIAITAAKHFKTNMYIAVACTAALV 187

Query: 183 HPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSAI 242
            P        G+ A   G+ FLGI ++   Y+SSV+P +F  W+ S +ER LN  +   +
Sbjct: 188 SPAWTEIA--GRVASGEGVTFLGIALSETVYTSSVLPPLFLVWILSYVERFLNKRIHEVV 245

Query: 243 KNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFVM 302
           K  F P +C++V+ P+T LL+GPLST  +  IA GY  L + VPA AGA++GGFWQ+ V+
Sbjct: 246 KPLFVPFICMVVMVPLTILLIGPLSTAGANGIANGYNVLAENVPALAGAIIGGFWQVLVI 305

Query: 303 FGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAALT 362
           FG+HWG+ P+ + NF   G D+       A++AQVGA LGV L  R+ + + V  SA +T
Sbjct: 306 FGVHWGITPMVLANFEQYGRDSFQAYQTIAVIAQVGAVLGVILKARNRETRKVGVSAGIT 365

Query: 363 SLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSF-GLPSIFTFMQTIPS 421
            LFGITEPA+YGV L  K PF+  CISGA+GA    +     +++ GLP   T +  I S
Sbjct: 366 GLFGITEPAIYGVTLRFKKPFIFGCISGAVGAIAASFFTPYYFAYAGLPGPLTIVNGISS 425

Query: 422 TGIDFTVWASVIGGVIAIGCAFVGTVMLHFI------TAKRQPAQGAPQEKTPEVITPP- 474
              DF    S+IG +I +  A +  V+L  +      T ++     + +++  E +    
Sbjct: 426 ---DFP--TSIIGILIGVAIALILPVVLIQMFGYGEDTVEQTAGATSDKDQVGEKMNASM 480

Query: 475 -EQGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHA 533
             +  I +P+ G+++PL  V D  F+SG +GKG AI P+  ++ +P  G +  L  T HA
Sbjct: 481 NNEETIPAPLAGKVLPLSEVPDAVFSSGAMGKGFAIEPTDNKLYAPFDGSVVMLAPTKHA 540

Query: 534 IGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTT 593
           IG+ S+ GVE+L+HVGIDTV LDG  F+ H+  G KV  GD L++FD  AI   G    T
Sbjct: 541 IGLRSEFGVELLVHVGIDTVSLDGSAFTLHIKEGSKVKKGDLLMTFDQEAIESKGLKTIT 600

Query: 594 PVLISNSDDFTDVLPHGTAQISAGEPLLSIIR 625
           PV+I+N+  + DV+    +   + + +++I++
Sbjct: 601 PVIITNTQAYEDVIVQEQSTCQSTDVMITIVK 632


Lambda     K      H
   0.324    0.141    0.427 

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: 1082
Number of extensions: 72
Number of successful extensions: 4
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: 625
Length of database: 632
Length adjustment: 38
Effective length of query: 587
Effective length of database: 594
Effective search space:   348678
Effective search space used:   348678
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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