GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Marivita geojedonensis DPG-138

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>NCBI__GCF_002115805.1:WP_085637757.1
          Length = 365

 Score =  206 bits (523), Expect = 1e-57
 Identities = 122/337 (36%), Positives = 190/337 (56%), Gaps = 17/337 (5%)

Query: 6   LDLAHSYKPNPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKV 65
           LD+ + YK      +   L  + +  E G    L+GPSGCGK+T+LN ++GL   + G +
Sbjct: 5   LDIKNLYK---SYGTTEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSI 61

Query: 66  LFDGRDVTRASPQERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEM 125
              G+D+T  SP++R+IA VFQ   +Y TMTVA+N+ F ++ R V +    +++  +A+ 
Sbjct: 62  NIGGKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQ 121

Query: 126 LEMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQI 185
           L++   LN+R   L+   +Q++++GR LVR D    LFDEPL+ +D  L+ ++R ++K +
Sbjct: 122 LQIEPLLNRRPGQLSGGQRQRVAMGRALVR-DPKLFLFDEPLSNLDAKLRVEMRTEIKSL 180

Query: 186 HHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGM 245
           HH L  +++YVTHDQ+EA+T A ++VVM  G   Q+GS   ++ RPA+ FV  F+GSP M
Sbjct: 181 HHNLGASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAM 240

Query: 246 NFLP--AHRDGENLSVAGHR-------LASPVGRALPAGALQVGIRPEYLA---LAQPQQ 293
           N +P  AHR  E   +   R       L     R LP   + +G+RPE +A   L   + 
Sbjct: 241 NLIPAKAHRADEGTRIEITRKSGEPIVLTDTKNRDLPEDVI-LGVRPEDIADPDLRGAEA 299

Query: 294 AGALPGTVVQVQDIGTYQMLTAKVGEHTVKARFTPET 330
           A A    +  V+  G       ++G   V AR   ET
Sbjct: 300 AQAAECLIDMVEPAGADTFAVMQLGGKHVTARLHAET 336


Lambda     K      H
   0.320    0.136    0.395 

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: 312
Number of extensions: 18
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: 358
Length of database: 365
Length adjustment: 29
Effective length of query: 329
Effective length of database: 336
Effective search space:   110544
Effective search space used:   110544
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: 49 (23.5 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