GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltP in Caulobacter crescentus NA1000

Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate CCNA_00264 CCNA_00264 C4-dicarboxylate transport protein

Query= SwissProt::P21345
         (437 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00264 CCNA_00264 C4-dicarboxylate
           transport protein
          Length = 417

 Score =  294 bits (752), Expect = 4e-84
 Identities = 175/423 (41%), Positives = 262/423 (61%), Gaps = 37/423 (8%)

Query: 9   AWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAG------------DIFIHLIKMIV 56
           A+ I+ +M+LG+L+G           W     L PAG            DIF+ LIKMI+
Sbjct: 6   AYLIIASMILGVLVG-----------WTCNQFLDPAGAKSAADNLSIITDIFLRLIKMII 54

Query: 57  VPIVISTLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQ 116
            P+V +TLV G+A + DA  +GRIGAKT+ +F   + V+++LG+ + ++  PGAG++M  
Sbjct: 55  APLVFTTLVAGVAHMEDAAAVGRIGAKTMTWFIGASAVSLVLGLLMVHLLDPGAGLNM-- 112

Query: 117 LATVDIS-KYQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLS 175
            A VD++ K  +TT+A       + G I  LVPT+I  +MAK E+L I+ FS+  G  ++
Sbjct: 113 -AHVDVAMKTTATTDAFT-----LKGFITHLVPTSIFDAMAKNEILQIVVFSLFVGTAVA 166

Query: 176 SLPATHREPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVL 235
           +L     + L  V ++ ++ M KVT  VM+ AP+ +FA +A T+A  G   L    K VL
Sbjct: 167 ALDDKAPQILELVEQA-AQIMLKVTGFVMKLAPLAIFAALASTIATQGLGMLATYGKFVL 225

Query: 236 LVHFA--ILFFALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEA 293
             + A  +L+  L + G++  + G  V  L  +++D ++LA+STASSE+  PRI++ +  
Sbjct: 226 GFYSAMGVLWALLFIAGLL--VLGKRVIPLFGVIRDPVLLAFSTASSEAAYPRILDSLPK 283

Query: 294 YGAPVSITSFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKG 353
            G    I SFV+P GYSFNLDGS LY + A +FI Q +G++L++ Q+I ++L LMVTSKG
Sbjct: 284 VGVRRRIVSFVLPLGYSFNLDGSMLYCTFATMFIVQAHGVELTVQQQIFMLLLLMVTSKG 343

Query: 354 IAGVPGVSFVVLLATLGSVGIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEH 413
           IAGVP  S VV++ATL   G+P   +A + GVD +LDM R+A NVVGN++A  V+AKWE 
Sbjct: 344 IAGVPRASLVVIMATLTYFGLPEAWIALVLGVDHLLDMGRSATNVVGNSVAAAVVAKWEG 403

Query: 414 KFD 416
           + D
Sbjct: 404 ELD 406


Lambda     K      H
   0.326    0.141    0.403 

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: 464
Number of extensions: 17
Number of successful extensions: 5
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: 437
Length of database: 417
Length adjustment: 32
Effective length of query: 405
Effective length of database: 385
Effective search space:   155925
Effective search space used:   155925
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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