GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Klebsiella michiganensis M5al

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate BWI76_RS07265 BWI76_RS07265 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Koxy:BWI76_RS07265
          Length = 239

 Score =  193 bits (491), Expect = 2e-54
 Identities = 102/229 (44%), Positives = 153/229 (66%), Gaps = 6/229 (2%)

Query: 16  NVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKN 75
           +VH G I+ V   + V+F V+ GE  T+IG NGAGKS+  + I GL  P +G+I F GK 
Sbjct: 11  SVHYGGIQAV---RDVSFSVKEGEQTTLIGANGAGKSSTVRAITGL-EPFSGEILFNGKP 66

Query: 76  IAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDK--IFAMFPRL 133
           I   ++  ++R G+  VP+   +F  ++V ENL+MGA++R D+    ++   IFA FPRL
Sbjct: 67  IRKRRAESLLREGLVMVPEGRGIFARMTVLENLQMGAWLRRDAAAVKQEMGAIFANFPRL 126

Query: 134 SDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEG 193
           ++R+ Q AG LSGGE+Q+LA+ +AL+ +P LL+LDEPS  L+P++V  +F  +  + Q G
Sbjct: 127 AERQHQLAGLLSGGEQQLLALNRALLSQPRLLILDEPSMGLAPLMVENIFRVIATLRQRG 186

Query: 194 TAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242
            A++L+EQNAR ALE  D  +V++SG     GP Q LL D ++A++YLG
Sbjct: 187 VALLLIEQNARLALEATDSAWVMDSGSIVERGPSQTLLADDRIAQIYLG 235


Lambda     K      H
   0.317    0.136    0.377 

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: 175
Number of extensions: 9
Number of successful extensions: 3
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: 247
Length of database: 239
Length adjustment: 23
Effective length of query: 224
Effective length of database: 216
Effective search space:    48384
Effective search space used:    48384
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