GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Nocardiopsis baichengensis YIM 90130

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_017540507.1 C892_RS0115120 hypothetical protein

Query= TCDB::Q8YXD0
         (288 letters)



>NCBI__GCF_000341205.1:WP_017540507.1
          Length = 470

 Score =  189 bits (479), Expect = 1e-52
 Identities = 114/299 (38%), Positives = 176/299 (58%), Gaps = 24/299 (8%)

Query: 7   QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFF------------- 53
           QL V G+  G IIA+++VGL+L +G  R+ NFAHGD +T GA++                
Sbjct: 166 QLTVAGLTFGLIIAISSVGLSLIFGTTRMINFAHGDMVTFGAFMAMMFANMTLFSSLHEV 225

Query: 54  -----VNTFGVN-IWLSMIVAVV--GTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLA 105
                V  F  N + L +++AVV  G +G  L  E+ LW  +R        + I++IG +
Sbjct: 226 FEGVPVLDFVFNPLVLGLVLAVVLGGALGAGL--ERFLWRPLRRRNVALIQMFIVTIGFS 283

Query: 106 LFLRNGIILIWGGRNQNY-NLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTK 164
           L LR+ +++++G R   Y    I  A ++  V +      +L +AV+ +  +  +LQ T+
Sbjct: 284 LVLRHMLLVVFGARRDKYPQFRIQEAWELGPVSITPRDAGILLVAVVVLVLVASMLQFTR 343

Query: 165 IGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLIL 224
           +GKAMRAVAD+ DLA+ SGIDV++V  + W + G +++LGG +YGL   V   MG+ L+L
Sbjct: 344 MGKAMRAVADNRDLAESSGIDVDRVTLYVWGLGGALSALGGVLYGLNATVHWQMGFHLLL 403

Query: 225 PLFASVILGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283
            +FA+VILGG+G  YGA+    ++G+V  +ST +   Q     AL IMILVLL+RP+G+
Sbjct: 404 LMFAAVILGGLGTAYGAMVGGLVVGLVAMLSTLWFSPQLMNVWALGIMILVLLVRPQGI 462


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: 333
Number of extensions: 17
Number of successful extensions: 3
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: 470
Length adjustment: 30
Effective length of query: 258
Effective length of database: 440
Effective search space:   113520
Effective search space used:   113520
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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