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_RS05975 BWI76_RS05975 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Koxy:BWI76_RS05975
          Length = 231

 Score =  201 bits (512), Expect = 8e-57
 Identities = 99/215 (46%), Positives = 152/215 (70%), Gaps = 1/215 (0%)

Query: 28  LQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVRL 87
           L+GV+  +   E+VT+IG NGAGK++    I  L+   TG++ F  ++I+  +++QIVR 
Sbjct: 17  LKGVDIDIHDREIVTLIGSNGAGKTSTLNGIVNLVRS-TGRVNFLNEDISRSQTHQIVRK 75

Query: 88  GMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFPRLSDRRRQRAGTLSGG 147
           G+  VP+   +F +L++EENL MGA+        L+D+++++FPRL +RR Q AGT+SGG
Sbjct: 76  GLALVPEGRRIFTNLTIEENLRMGAYNNLAGFPRLRDRMYSLFPRLKERRTQMAGTMSGG 135

Query: 148 ERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAIILVEQNARKAL 207
           E+QMLA+ +ALM EP LL+LDEPS  L+P +V ++F  +KQ+ +E   ++LVEQNA  AL
Sbjct: 136 EQQMLAIARALMSEPVLLMLDEPSLGLAPKIVGELFATIKQLREENITVLLVEQNATAAL 195

Query: 208 EMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242
            +ADR YVLE+G+  +SGP  E+L +P++  +YLG
Sbjct: 196 TIADRAYVLENGKIMLSGPAAEVLANPEIKRMYLG 230


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: 169
Number of extensions: 5
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: 247
Length of database: 231
Length adjustment: 23
Effective length of query: 224
Effective length of database: 208
Effective search space:    46592
Effective search space used:    46592
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.

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