Aligments for a candidate for cycA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for cycA in Paraburkholderia bryophila 376MFSha3.1

Align L-alanine and D-alanine permease (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_04042 H281DRAFT_04042
           aromatic amino acid:proton symporter, AAT family
          Length = 506

 Score =  405 bits (1040), Expect = e-117
 Identities = 198/441 (44%), Positives = 287/441 (65%), Gaps = 4/441 (0%)

Query: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77
           LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y IGG+   +IMR LGEM 
Sbjct: 55  LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 114

Query: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137
              PVAGSFS +A  Y G   GFL+GWNYW L+++  +AE+TAV  Y+  W+P VP W+ 
Sbjct: 115 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 174

Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197
           AL     + +INL  VKA+GE EFWFA+IK+V +I M++ G  ++  G G  G    ISN
Sbjct: 175 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG--GPQASISN 232

Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257
           LW+HGGF P+G  G+   L ++MF++ G+E+IG+TA EA  PQK+IP A+  V +RIL+F
Sbjct: 233 LWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 292

Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317
           Y+ +L V+LS+YPWNE+   GSPFVM F ++G    A ++N VV+TAALS  N G+++  
Sbjct: 293 YICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 352

Query: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377
           RMLY LA+ G AP    K    GVP  A+ LS  A    V++NYL+P +    + ++   
Sbjct: 353 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 412

Query: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437
             +  W +I L  LK R+++ A+    L ++ + +PVS+++ LAF+ L++ ++A  P   
Sbjct: 413 ALVLNWALISLTHLKSRRAMVAAGE-TLVFKSFWFPVSNWICLAFMALILVILAMTPGLS 471

Query: 438 VALYVGPAFLVLLTVLFYTFK 458
           V++ + P +LV++    Y FK
Sbjct: 472 VSVLLVPVWLVVMWA-GYAFK 491


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: 694
Number of extensions: 30
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: 473
Length of database: 506
Length adjustment: 34
Effective length of query: 439
Effective length of database: 472
Effective search space:   207208
Effective search space used:   207208
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources