GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Methanospirillum stamsii Pt1

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_109939172.1 DLD82_RS00420 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_774
         (244 letters)



>NCBI__GCF_003173335.1:WP_109939172.1
          Length = 376

 Score =  152 bits (385), Expect = 7e-42
 Identities = 93/243 (38%), Positives = 141/243 (58%), Gaps = 12/243 (4%)

Query: 5   KNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVDGTS 64
           K + +  G    L + S  VKKGE+ V+ G SG GKSTL++C+N L     G +++DG  
Sbjct: 12  KEIRERTGHVVALKNISFSVKKGEIFVLMGLSGCGKSTLLRCLNRLISPTAGSILLDGED 71

Query: 65  IADPKTNLPKL--RSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQLLE 122
           IA   T   +   RSR+GMVFQ F L PH +I DN+    +++ G S EE +  A + L+
Sbjct: 72  IASVSTERMRTIRRSRMGMVFQSFALLPHKNIQDNVAFG-LEIQGISAEERAGIAKETLD 130

Query: 123 RVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDP----EMVNEVLDV 178
            VGLS +   +P QLSGG +QRV +ARA+A  P ++L DE  SALDP    +M NE+LD+
Sbjct: 131 LVGLSGYENSYPDQLSGGMKQRVGLARAIASSPDILLMDEAFSALDPMIRRDMQNELLDI 190

Query: 179 MVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDITARSDRAQHFL 238
             +L     T++ V+H++  A K+  R+  M  G+I++    EE       +++  + F+
Sbjct: 191 QDRLE---KTIIFVSHDLDEALKLGTRIGLMKAGEIVQIGTPEEIL--TQPKNEFVERFV 245

Query: 239 EKI 241
           E +
Sbjct: 246 EDV 248


Lambda     K      H
   0.321    0.135    0.390 

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: 217
Number of extensions: 12
Number of successful extensions: 4
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: 376
Length adjustment: 27
Effective length of query: 217
Effective length of database: 349
Effective search space:    75733
Effective search space used:    75733
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: 48 (23.1 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