GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Marinobacter adhaerens HP15

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 GFF2059 HP15_2015 inner-membrane translocator

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__Marino:GFF2059
          Length = 298

 Score =  125 bits (315), Expect = 9e-34
 Identities = 90/292 (30%), Positives = 149/292 (51%), Gaps = 15/292 (5%)

Query: 4   QTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAY-----LTFFVNTFG 58
           Q + ++V+G    S + + + GLTL YG++R+ N +HG F  LGAY     + ++ +T  
Sbjct: 3   QLLAILVDGSVYASWLFIISAGLTLIYGVMRILNMSHGSFYALGAYSGAAMVGWYFSTGS 62

Query: 59  VNIWLSMIV----AVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIIL 114
           V  W S +     A+V  + V LL E+ L   M     +   +I+++ G+ L + + I L
Sbjct: 63  VP-WFSFVALIAAALVAGISVGLLVERGLLRFMYG--RDEVVMILVTYGVLLIMEDAIKL 119

Query: 115 IWGGRNQNYNLPIT--PALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAV 172
           IWG        P T        G+       +++ +++L   AL Y L  T+ GK +R V
Sbjct: 120 IWGVEPYFAYQPYTLLGRTKFAGLSFANYDFMLIGVSILIGLALWYGLNRTRNGKLLRVV 179

Query: 173 ADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVIL 232
             D ++A   GI+V ++   T+LI   + SL G++     +V P MG  +I+  FA V++
Sbjct: 180 IHDREIASALGINVARIFTITFLIGAGIGSLAGALTAPGLSVVPGMGIEVIVLAFAVVVI 239

Query: 233 GGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284
           GG+G+  GA+  A I+G +   +   L    +  V   +M LVL  RP+GLF
Sbjct: 240 GGLGSITGALVGALIVG-MSRAAAVHLYPDVELFVIYAVMGLVLAFRPQGLF 290


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: 256
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: 298
Length adjustment: 26
Effective length of query: 262
Effective length of database: 272
Effective search space:    71264
Effective search space used:    71264
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 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:

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