GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacK in Magnetospirillum magneticum AMB-1

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383734.1 AMB_RS06730 nitrate ABC
           transporter ATP-binding protein
          Length = 452

 Score =  137 bits (345), Expect = 6e-37
 Identities = 103/302 (34%), Positives = 151/302 (50%), Gaps = 36/302 (11%)

Query: 2   ARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVT 61
           A L L  V K +      +   +E +   +++GE + L+G SG GKST LR+MAGL    
Sbjct: 9   ALLDLRGVRKTFLTPDRRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKAN 68

Query: 62  EGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVE 121
            GE++    ++ G +   + I+MVFQS+AL+P  +V  N+  GLE + G+   E  +R  
Sbjct: 69  GGEVKYRGHLMTGPA---KGISMVFQSFALFPWLTVEENVELGLE-AAGVAKAEREERAN 124

Query: 122 ETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTE 181
           E  D++G+       P +LSGG +QRV   RA+V  P+V L+DEP S LD      +R +
Sbjct: 125 EAIDLIGLGGYESAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLRED 184

Query: 182 LQRLQGELGVTT---VYVTHDQTEAMTMGDRVAVL--DDGELQ---QVGTPLDCYHRPNN 233
           L  L  E  + T   + V+H+  EA++M DRV V   D G ++   +V  P     RP +
Sbjct: 185 LLELWDERKIPTKGILLVSHNIEEAVSMADRVLVFSSDPGRVRAEIRVNLP-----RPRD 239

Query: 234 LFVAGF--IGEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTV 291
              A F  I +    L   ++     RG G            LG A  LTLG R  D T 
Sbjct: 240 TESAAFRQIVDEVYTLMTANV-----RGGG------------LGAAEQLTLGYRLPDTTP 282

Query: 292 GE 293
           G+
Sbjct: 283 GK 284


Lambda     K      H
   0.316    0.136    0.384 

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: 470
Number of extensions: 27
Number of successful extensions: 5
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: 383
Length of database: 452
Length adjustment: 31
Effective length of query: 352
Effective length of database: 421
Effective search space:   148192
Effective search space used:   148192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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