GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cycA in Pseudomonas simiae WCS417

Align L-alanine and D-alanine permease (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>lcl|FitnessBrowser__WCS417:GFF4632 PS417_23700 aromatic amino acid
           transporter
          Length = 467

 Score =  402 bits (1033), Expect = e-116
 Identities = 198/446 (44%), Positives = 286/446 (64%), Gaps = 12/446 (2%)

Query: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77
           LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y I G    +IMR LGEM 
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70

Query: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137
           V  PVAGSFS +A  Y G  AGFL GWNYW L+++  +AE+TAV  Y+  W+PD+P W+ 
Sbjct: 71  VEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWVS 130

Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197
           AL   V++  IN + VK FGE EFWFA+IK+V I+ M++ G  ++  G G  G    +SN
Sbjct: 131 ALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTG--GPQASVSN 188

Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257
           LW+HGGF PNG  G+LMS+  +MF++ G+E++G+TA EA  P+K IP AI  V +RIL+F
Sbjct: 189 LWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRILIF 248

Query: 258 YVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFVVITAALSS 308
           YVGAL V+LS+YPW+++            GSPFV  F  +G  TAA I+NFVV+TAALS 
Sbjct: 249 YVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAALSV 308

Query: 309 CNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVF 368
            N G++   RML+ LA+ G AP    K +  GVP RAL +S    +L V++NY+ P+   
Sbjct: 309 YNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQSAL 368

Query: 369 VWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVG 428
             + ++     +  W +I +  +KFRK++   +     ++ + +P S+YL LAF+V+++ 
Sbjct: 369 ELLFALVVASLMINWALISITHIKFRKAM-GEQGVTPSFKTFWFPFSNYLCLAFMVMIIS 427

Query: 429 LMAYFPDTRVALYVGPAFLVLLTVLF 454
           +M   P    ++Y  P ++ ++ V +
Sbjct: 428 VMLAIPGISESVYAMPVWVGIIYVAY 453


Lambda     K      H
   0.328    0.142    0.444 

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: 663
Number of extensions: 45
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: 473
Length of database: 467
Length adjustment: 33
Effective length of query: 440
Effective length of database: 434
Effective search space:   190960
Effective search space used:   190960
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.

Links

Downloads

Related tools

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 preprint 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