GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas fluorescens FW300-N1B4

Align D-serine/D-alanine/glycine transporter (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP

Query= SwissProt::P0AAE0
         (470 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559
          Length = 473

 Score =  344 bits (882), Expect = 4e-99
 Identities = 178/460 (38%), Positives = 278/460 (60%), Gaps = 19/460 (4%)

Query: 19  LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78
           L+R L NRHIQLIA+GGAIGTGLF+GS   +  AGPS+I  Y I GF+ F +MR +GE++
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70

Query: 79  LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVA 138
           +      SFS FA    G +AG+ +GW  W  +++ GM+++ A+  Y  +W PD+  WV+
Sbjct: 71  VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWVS 130

Query: 139 SLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASFA 198
           +    VL+  +NLA VK+FGE EFWFA+IK+VAIV +I +G  ++        G +AS  
Sbjct: 131 AAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLV---SGDGGPQASVT 187

Query: 199 HLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRIIM 258
           +LW  GG+FP G+SG      I +F+F G+E++G TAAE   P+  +P+AIN +  RI++
Sbjct: 188 NLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILI 247

Query: 259 FYVFALIVIMSVTPWSSVVP---------EKSPFVELFVLVGLPAAASVINFVVLTSAAS 309
           FY+ AL+V++S+TPW S++            SPFV++F ++G   AA ++NFVVLT+A S
Sbjct: 248 FYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAALS 307

Query: 310 SANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVI 369
             NSG +  SRML G+A++G APKA +K+ KR VP + +  S    L  V++ Y+ P   
Sbjct: 308 VYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLNYLVPQ-- 365

Query: 370 GAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFV 429
            A  ++ ++     +  W +I  S+  +R+      +  ++K        +VC+AF VF+
Sbjct: 366 HALELLMSLVVATLVINWAMISFSHFKFRQHMNKTKQTPLFKALWYPYGNYVCLAFVVFI 425

Query: 430 VVLLTLEDDTRQALLVTPLWFIALGLGWLFIG--KKRAAE 467
           + ++ L    + ++   P+W   +   W+  G   KR+A+
Sbjct: 426 LGVMLLIPGIQISVYAIPVW---VAFMWVCYGIKNKRSAQ 462


Lambda     K      H
   0.329    0.141    0.440 

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: 596
Number of extensions: 34
Number of successful extensions: 6
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: 470
Length of database: 473
Length adjustment: 33
Effective length of query: 437
Effective length of database: 440
Effective search space:   192280
Effective search space used:   192280
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 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