GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Methanobacterium arcticum M2

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate WP_048081634.1 EI99_RS08980 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_16275
         (244 letters)



>NCBI__GCF_000746075.1:WP_048081634.1
          Length = 229

 Score =  150 bits (379), Expect = 2e-41
 Identities = 92/221 (41%), Positives = 135/221 (61%), Gaps = 7/221 (3%)

Query: 1   MISIKNVNKWY--GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDV 58
           +I IK + K Y  G  + L     E++KGE + + GPSGSGKSTL+  + AL+   +G V
Sbjct: 6   IIEIKGLKKSYDKGKIKALNGIDLEIRKGEFVSIIGPSGSGKSTLLNMIGALDTAGEGSV 65

Query: 59  VVDGTSIADPKTDLPKLRSR-VGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKG 117
            V G  +   K DL K RS+ +G VFQ   L P+LT+ EN+ I  I     S ++  K+ 
Sbjct: 66  EVAGIDLTKTK-DLSKFRSQEIGFVFQLHNLIPNLTVLENVQIPMIGT-SISGKDMEKRA 123

Query: 118 LQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLD 177
           L+LL+ V L     + P +LSGG++QRVAIARAL  +P ++L DEPT ALD +  + +LD
Sbjct: 124 LKLLKSVDLEDRIDQRPTKLSGGERQRVAIARALVNNPSIILADEPTGALDSKTGDIILD 183

Query: 178 VMVQL-ANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIED 217
           ++  L   E +T++ VTHE  +   +ADR+I +  GKI+E+
Sbjct: 184 LLKDLHKKENVTLVMVTHE-PYVANMADRIITVRDGKILEE 223


Lambda     K      H
   0.321    0.136    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: 140
Number of extensions: 8
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: 244
Length of database: 229
Length adjustment: 23
Effective length of query: 221
Effective length of database: 206
Effective search space:    45526
Effective search space used:    45526
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 (21.8 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