GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Methanobacterium arcticum M2

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_048081634.1 EI99_RS08980 ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_000746075.1:WP_048081634.1
          Length = 229

 Score =  144 bits (363), Expect = 2e-39
 Identities = 90/224 (40%), Positives = 137/224 (61%), Gaps = 9/224 (4%)

Query: 15  EVAVEIVNMNKWY--GDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKG 72
           E  +EI  + K Y  G    L  I+L++ +GE + I GPSGSGKST++  I  L+   +G
Sbjct: 4   ENIIEIKGLKKSYDKGKIKALNGIDLEIRKGEFVSIIGPSGSGKSTLLNMIGALDTAGEG 63

Query: 73  KIVVDGTELTN--DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAE 130
            + V G +LT   DL K     +E+G VFQ  NL P+LT+LEN  + P+    +  K  E
Sbjct: 64  SVEVAGIDLTKTKDLSKFRS--QEIGFVFQLHNLIPNLTVLENVQI-PMIGTSISGKDME 120

Query: 131 EVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKE 190
           + A+  LK V + ++ ++ P +LSGG++QRVAIAR+L  NP I+L DEPT ALD +    
Sbjct: 121 KRALKLLKSVDLEDRIDQRPTKLSGGERQRVAIARALVNNPSIILADEPTGALDSKTGDI 180

Query: 191 VLDTMVGL-AEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQ 233
           +LD +  L  +E +T++ VTHE  +   +A+R+I +  G+I+E+
Sbjct: 181 ILDLLKDLHKKENVTLVMVTHE-PYVANMADRIITVRDGKILEE 223


Lambda     K      H
   0.321    0.135    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: 141
Number of extensions: 10
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: 257
Length of database: 229
Length adjustment: 23
Effective length of query: 234
Effective length of database: 206
Effective search space:    48204
Effective search space used:    48204
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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