GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Mesorhizobium ciceri WSM1271

Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate YP_004144924.1 Mesci_5852 sodium:dicarboxylate symporter

Query= CharProtDB::CH_088342
         (421 letters)



>NCBI__GCF_000185905.1:YP_004144924.1
          Length = 452

 Score =  338 bits (868), Expect = 1e-97
 Identities = 163/406 (40%), Positives = 265/406 (65%), Gaps = 9/406 (2%)

Query: 9   QIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68
           Q+   + LG+ VG ++ G  +    L+P+GD F++L+KMI+ P++  ++  G+A + DLK
Sbjct: 43  QVLTAIALGVAVGYLYPGTGEA---LKPLGDAFIKLVKMIIAPVIFLTVTTGIAGMNDLK 99

Query: 69  KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMK--SLEKTDIQSYVDTTNEVQ 126
           K+G++ GK +IYF   +++A++VGL+ AN+ QPG+G+++   SL+   +Q YV    +V 
Sbjct: 100 KVGRVAGKAMIYFLTFSSLALMVGLVVANVVQPGSGLDIDPASLDGQAVQGYVA---KVH 156

Query: 127 HHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAM 186
             S+    +NI+P  I  + + G++L ++FFS++FG  +A  G+ GKPVL   Q     +
Sbjct: 157 DQSVTGFLMNIIPSTIVGAFAEGNILQVLFFSILFGSALAMAGDTGKPVLSLLQALLAPV 216

Query: 187 FYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLF 246
           F +   +M+ AP G F  +  T+ K+G+ S++ L+ LV   Y T   F+F +LG V +  
Sbjct: 217 FKLVGILMQAAPVGAFGAMAFTIGKYGIGSVVNLAMLVATFYFTAFVFVFGILGAVCRYN 276

Query: 247 GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGS 306
           G +IF +++ +K+EL+L  +T+SSE  LP +M+KMEK G  +++   VIPTGYSFNLDG+
Sbjct: 277 GFSIFSLVRYIKEELLLVLATSSSEAALPSLMEKMEKAGAKRSVVGLVIPTGYSFNLDGT 336

Query: 307 TLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIP 365
            +Y  LAA+FIAQ     +SV+ QI LL+V M++SKG AG+ G  FV L ATL  +  +P
Sbjct: 337 NIYMTLAALFIAQATNTHLSVADQILLLVVAMLSSKGAAGITGAGFVTLAATLSVIPTVP 396

Query: 366 VEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGK 411
           V G+A I G+DR +   R   NV+GN++AA+++++WEG+ +E + K
Sbjct: 397 VAGMALILGVDRFMSECRALTNVVGNAVAALVVARWEGELDEARMK 442


Lambda     K      H
   0.326    0.143    0.402 

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: 400
Number of extensions: 18
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: 421
Length of database: 452
Length adjustment: 32
Effective length of query: 389
Effective length of database: 420
Effective search space:   163380
Effective search space used:   163380
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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