GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Klebsiella michiganensis M5al

Align ABC transporter (characterized, see rationale)
to candidate BWI76_RS26290 BWI76_RS26290 glycerol-3-phosphate ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>FitnessBrowser__Koxy:BWI76_RS26290
          Length = 356

 Score =  342 bits (877), Expect = 9e-99
 Identities = 183/356 (51%), Positives = 253/356 (71%), Gaps = 8/356 (2%)

Query: 1   MIKLKLDNVNKQLGGM-RILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59
           M  LKL  V K   G  ++++ ++L++A GEF+V VGPSGCGKSTLLR++AGL+ +  GD
Sbjct: 1   MAGLKLQAVTKSWDGKTQVIQPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTSGD 60

Query: 60  LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119
           + ID +RV ++EP++RG+ MVFQ+YALYPHMSV +N+++GLK+    K  + ERV + A+
Sbjct: 61  IWIDRKRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGLGKGLIAERVQEAAR 120

Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179
           IL+LD LL+R+P+ELSGGQRQRVAMGRA+ R+P + LFDEPLSNLDA LRVQMR E+  L
Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQHL 180

Query: 180 HDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRM 239
           H RL +T +YVTHDQVEAMTLA +++V+N G  EQ+G+P E+YE+PASRFVA F+GSP M
Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNKGVAEQIGTPVEVYEKPASRFVASFIGSPAM 240

Query: 240 NFLSARLQTPGETSLVDTLVWGITSLPFDSSNLA-AGTPLSLGIRPEHVSLKA-ADGTAG 297
           N L  R+   G       L  G+  LP +S +   AG  ++LGIRPEH +L + A+G   
Sbjct: 241 NLLEGRVSDDGSRF---ELAGGML-LPINSEHRRYAGRKMTLGIRPEHFALSSQAEGGVP 296

Query: 298 VVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDAD 353
           +V+  +E LG++   H   G ++ L+ R       QAG  + L L  ++LHLFD++
Sbjct: 297 LVMDTLEILGADNLAHGRWG-EQKLVVRLPHQQRPQAGSTLWLHLPQESLHLFDSE 351


Lambda     K      H
   0.320    0.137    0.394 

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: 375
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: 381
Length of database: 356
Length adjustment: 30
Effective length of query: 351
Effective length of database: 326
Effective search space:   114426
Effective search space used:   114426
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.

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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