GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Cupriavidus basilensis 4G11

Align Amino acid:proton symporter (characterized, see rationale)
to candidate RR42_RS26130 RR42_RS26130 C4-dicarboxylate ABC transporter

Query= uniprot:A0A0N9WTL5
         (431 letters)



>FitnessBrowser__Cup4G11:RR42_RS26130
          Length = 436

 Score =  525 bits (1353), Expect = e-154
 Identities = 269/406 (66%), Positives = 325/406 (80%), Gaps = 1/406 (0%)

Query: 1   MKKNKLPRRIAMGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLV 60
           MK NKL  RI + + LG++ G+ C+ F      AKEIASYFS+VTD+FLR+IKMIIAPLV
Sbjct: 1   MKANKLTTRIMIAMVLGIVTGYLCNRFVPDAAMAKEIASYFSIVTDVFLRLIKMIIAPLV 60

Query: 61  FATLVGGIASMGNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHA 120
           F TLV GIA M ++ +VGRIG +A+ WF+TAS++SLL+GM  V+L QPG  LN+ + +  
Sbjct: 61  FGTLVAGIAGMKDASAVGRIGIKALGWFITASLLSLLLGMFFVDLLQPGHALNLPLPEIG 120

Query: 121 TAAVPVNTGDFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRIT 180
           TA   + T   +LK FI HVFP+S+ EAMA NEILQI+VFSLFFGFA+A  K      + 
Sbjct: 121 TAT-NLKTSTLNLKDFITHVFPKSVFEAMAQNEILQILVFSLFFGFAIASFKGKVGHHLV 179

Query: 181 DSIEELAKVMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILILWA 240
            SIEEL  +M ++TD+VM FAP+GVFAA+A+AIT QG+G+L  YGK I  FYLG+L+LW 
Sbjct: 180 ASIEELVAIMLRVTDFVMRFAPLGVFAAVAAAITVQGIGVLFTYGKFIGGFYLGLLVLWL 239

Query: 241 LLFGAGYLFLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLP 300
           +L  AGYLFLG  VF L KLIREP +LAFSTASSE+AYPKT+E +EKFG P +V+ FVLP
Sbjct: 240 VLTAAGYLFLGGRVFTLLKLIREPTILAFSTASSEAAYPKTMEQMEKFGVPNKVTGFVLP 299

Query: 301 LGYSFNLDGSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMITSKGMAGVARASVVVVA 360
           LGYSFNLDGSMMYQAFA LFIAQAYNI++S TQQ+ +LL LM+TSKG+AGV RAS+VVVA
Sbjct: 300 LGYSFNLDGSMMYQAFAALFIAQAYNIEMSLTQQITMLLVLMVTSKGIAGVPRASIVVVA 359

Query: 361 ATLPMFNLPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSE 406
           ATLPMFNLPEAGLLLI+GIDQFLDM RTATNV+GNSIATAVVAK E
Sbjct: 360 ATLPMFNLPEAGLLLILGIDQFLDMGRTATNVIGNSIATAVVAKWE 405


Lambda     K      H
   0.325    0.138    0.392 

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: 547
Number of extensions: 23
Number of successful extensions: 2
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: 431
Length of database: 436
Length adjustment: 32
Effective length of query: 399
Effective length of database: 404
Effective search space:   161196
Effective search space used:   161196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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 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