GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Klebsiella michiganensis M5al

Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate BWI76_RS09500 BWI76_RS09500 arginine ABC transporter substrate-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09900
         (251 letters)



>FitnessBrowser__Koxy:BWI76_RS09500
          Length = 243

 Score =  189 bits (479), Expect = 6e-53
 Identities = 106/245 (43%), Positives = 147/245 (60%), Gaps = 6/245 (2%)

Query: 5   KKFLLAAAVSLVFSANAMAADKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKV 64
           KK +LAA +S  F+  A AA+K+  G+ A YPPF + DA+ Q+ GFD D+ +ALC +M+ 
Sbjct: 2   KKLVLAALLSS-FAFGAAAAEKISFGVSATYPPFESMDANNQIAGFDIDLANALCKQMQA 60

Query: 65  ECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAEFK 124
           EC      +D +IPAL  KK+D +IS + IT  R + V FTDPYY+N    I+ K A   
Sbjct: 61  ECTFTNHAFDSLIPALKFKKYDAVISGMDITPGRSKQVAFTDPYYANSALVISKKDAFHS 120

Query: 125 TDKDSLKGKVIGAQRATLAGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILADKYV 184
              D LKGK IG +  T    +L+D+   ++ T  YD+ +NA++DL +GR+D +  D  V
Sbjct: 121 F--DDLKGKRIGMENGTTHQKYLQDK-HPEVKTVAYDSYQNAFIDLKNGRIDGVFGDTAV 177

Query: 185 NYDWLKT--EAGRAYEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKKIN 242
             +WLKT  + G A     D       +GIAVR  +  L  KLNAALK I ADGTY KI+
Sbjct: 178 VNEWLKTNPQLGAATPKVTDAQYFGTGLGIAVRPDNKALLEKLNAALKAIKADGTYDKIS 237

Query: 243 DKYFP 247
            ++FP
Sbjct: 238 KQWFP 242


Lambda     K      H
   0.316    0.133    0.381 

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: 186
Number of extensions: 10
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: 251
Length of database: 243
Length adjustment: 24
Effective length of query: 227
Effective length of database: 219
Effective search space:    49713
Effective search space used:    49713
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 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