GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Pantoea rwandensis LMG 26275

Align histidine permease (characterized)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter

Query= reanno::pseudo3_N2E3:AO353_12275
         (468 letters)



>NCBI__GCF_002095475.1:WP_084934657.1
          Length = 463

 Score =  375 bits (962), Expect = e-108
 Identities = 189/442 (42%), Positives = 273/442 (61%), Gaps = 3/442 (0%)

Query: 8   LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67
           L+R L  RHI+ +A+G AIGTGLF GS   I +AGP+++  Y+I G  +F VMRA+GE+ 
Sbjct: 18  LRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 77

Query: 68  VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127
           + N    SF  +A+  LGP AG+  GWTY F  V+ G+ADV A   Y   WFP  S W+ 
Sbjct: 78  LSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPGFSIWMS 137

Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187
            L  +     LN+  VK+FGEMEFW +++K+ AIVA+I+ G  ++     +  G    +S
Sbjct: 138 ALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYPSPNGTTASLS 197

Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247
           N+W  GG  P G+ G  A F + +FAF GIE++G  A E KDP  VLPRAINA+P+RI++
Sbjct: 198 NIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRAINAIPVRIIM 257

Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307
           FYVL +LV+M++ PW Q+    SPFV++F  +G+ +AA+I+N VV+T+A S+ NS IF  
Sbjct: 258 FYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTSAASSANSGIFST 317

Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPE--NVFLLIASI 365
            RM+FGLA+ G A K F  LS   VP   +    + LL+GV L YLIP+   VF ++ ++
Sbjct: 318 SRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDVMTVFTMVTTV 377

Query: 366 ATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFP 425
           +    ++VW +IL + +A R+       A  KF +P   +     +AF  FV  +L    
Sbjct: 378 SAILFMFVWTIILCSYLAYRKQHPQRHAAS-KFKMPLGKFMCWVCMAFFAFVLVLLTLQE 436

Query: 426 DTQAALIVGVVWIVLLVLAYLM 447
           DT+ AL+V  +W V+L L +L+
Sbjct: 437 DTRQALMVTPLWFVILTLGWLL 458


Lambda     K      H
   0.329    0.142    0.441 

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: 650
Number of extensions: 36
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: 468
Length of database: 463
Length adjustment: 33
Effective length of query: 435
Effective length of database: 430
Effective search space:   187050
Effective search space used:   187050
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 (21.8 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