GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Shewanella loihica PV-4

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 5210165 Shew_2609 inner-membrane translocator (RefSeq)

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__PV4:5210165
          Length = 297

 Score =  125 bits (314), Expect = 1e-33
 Identities = 86/292 (29%), Positives = 157/292 (53%), Gaps = 22/292 (7%)

Query: 6   IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGA-----YLTFFVNTFGVN 60
           IQLI+NG+ VG +  +  +   L Y   ++ NFA G+FL +GA     +LT+F   F V 
Sbjct: 7   IQLIINGLIVGLLYGVVGMCFVLVYKSTQIVNFAQGEFLLVGAWVCWAFLTYFQLPFFVG 66

Query: 61  IWLSM-IVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGR 119
              ++  +AV G +  M++   ++   + S+       I+++IGL++F ++    I+G  
Sbjct: 67  FLFTLCFMAVFGVLLQMIVLRPMIGEPIISV-------IMVTIGLSIFFQSLTKWIFGVS 119

Query: 120 NQNYNLPI-TPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDL 178
            Q+Y     T ++ IFG+ +    L+   +A+L + A     + +K G AMRA A D  +
Sbjct: 120 PQSYPQVFDTQSIAIFGLNIELAYLMSTVIAILIMAAFFLFFKYSKHGLAMRATAFDQQV 179

Query: 179 AKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNP 238
           A+  GI V+QV   +W IA TV++  G + G++  V  ++   + + +F +VILGG+ + 
Sbjct: 180 AQSLGISVKQVFAMSWGIAATVSATAGVVIGMVNGVSDSLS-TIGIKVFPAVILGGLDSI 238

Query: 239 YGAIAAAFIIGIVQEVSTPF------LGSQYKQGVALLIMILVLLIRPKGLF 284
            GAI    +IG+++ ++  F      +G+ Y       +++++L  +P GLF
Sbjct: 239 VGAIVGGVVIGVLENIAEFFDSQWLHIGNMY-DIAPFYVLLVILWFKPYGLF 289


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: 280
Number of extensions: 13
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: 297
Length adjustment: 26
Effective length of query: 262
Effective length of database: 271
Effective search space:    71002
Effective search space used:    71002
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