GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatJ in Klebsiella michiganensis M5al

Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate BWI76_RS08110 BWI76_RS08110 glutamate/aspartate ABC transporter substrate-binding protein

Query= CharProtDB::CH_002441
         (302 letters)



>FitnessBrowser__Koxy:BWI76_RS08110
          Length = 303

 Score =  537 bits (1383), Expect = e-157
 Identities = 267/303 (88%), Positives = 286/303 (94%), Gaps = 1/303 (0%)

Query: 1   MQLRKPATAILALALSAGLAQADDAAPAAG-STLDKIAKNGVIVVGHRESSVPFSYYDNQ 59
           MQLRK A A+L + L+AG A A+DAA  AG STLDKIAKNGVIVVGHRESSVPFSYYDN+
Sbjct: 1   MQLRKLAAAMLVMGLTAGAAHAEDAASTAGQSTLDKIAKNGVIVVGHRESSVPFSYYDNK 60

Query: 60  QKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVE 119
           Q+VVGYSQDYSNAIV+A+KKKLNKPDLQ+KLIP+TSQNRIPLLQNGT+DFECGSTTNN+E
Sbjct: 61  QQVVGYSQDYSNAIVDAIKKKLNKPDLQIKLIPVTSQNRIPLLQNGTYDFECGSTTNNLE 120

Query: 120 RQKQAAFSDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNM 179
           RQKQAAFSDTIFVVGTRLL KKGG IKDF +LKDKAVVVTSGTTSE+LL+KLN+E+KMNM
Sbjct: 121 RQKQAAFSDTIFVVGTRLLVKKGGAIKDFPDLKDKAVVVTSGTTSEILLHKLNDEKKMNM 180

Query: 180 RIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLR 239
           RIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVG  QSQEAYGCMLR
Sbjct: 181 RIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGTAQSQEAYGCMLR 240

Query: 240 KDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDK 299
           KDDPQFK L+DDT+A VQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFK PNDK
Sbjct: 241 KDDPQFKTLVDDTVAHVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKSPNDK 300

Query: 300 ALN 302
           ALN
Sbjct: 301 ALN 303


Lambda     K      H
   0.314    0.130    0.366 

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: 422
Number of extensions: 7
Number of successful extensions: 1
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: 302
Length of database: 303
Length adjustment: 27
Effective length of query: 275
Effective length of database: 276
Effective search space:    75900
Effective search space used:    75900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 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