GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Desulfatiglans anilini DSM 4660

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_028321170.1 H567_RS0109125 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8YXD0
         (288 letters)



>NCBI__GCF_000422285.1:WP_028321170.1
          Length = 308

 Score =  152 bits (383), Expect = 1e-41
 Identities = 89/288 (30%), Positives = 160/288 (55%), Gaps = 15/288 (5%)

Query: 9   IVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGV--------- 59
           ++NG+ +G I AL A+G TL YGIL + NFAHG+    G++  +   TF +         
Sbjct: 14  LINGLTIGGIYALIALGYTLVYGILFMINFAHGEIFMFGSFAGYAALTFLLQYGFTEQRP 73

Query: 60  --NIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWG 117
             +I  + + A+V +  +  + E++ +  +R  RA+    +I +IG ++FL+N +++I  
Sbjct: 74  LASILAAFLAAMVVSALLGTILERIAYRPLR--RASRLAPLISAIGASIFLQNVMLIIIK 131

Query: 118 GRNQNY-NLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDL 176
           GR Q Y +L      +I    +   Q++++  +   +  L+  +Q T+ G+AMRAVA+D 
Sbjct: 132 GRMQVYPDLLHETFFEIGWFNISNFQIMIILGSFFLMAGLYIFIQRTRTGRAMRAVAEDR 191

Query: 177 DLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLI-TAVRPNMGWFLILPLFASVILGGI 235
             A + GIDV ++I  T++I   + +  G M G+  T +   MG+   +  F + +LGGI
Sbjct: 192 SAAALMGIDVNRIIMITFVIGSALAAAAGVMVGMYYTQINHMMGFIPGIKAFTAAVLGGI 251

Query: 236 GNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283
           GN  GA+     +G+ +     F+ +QYK  +A  +++LVL+ RP+G+
Sbjct: 252 GNVPGAMLGGLFLGLAEAFGVLFMPAQYKDVIAFALLVLVLIFRPRGI 299


Lambda     K      H
   0.328    0.144    0.426 

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: 221
Number of extensions: 11
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: 288
Length of database: 308
Length adjustment: 26
Effective length of query: 262
Effective length of database: 282
Effective search space:    73884
Effective search space used:    73884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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