GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kdaD in Sinorhizobium meliloti 1021

Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate SMa0247 SMa0247 hypothetical protein

Query= reanno::HerbieS:HSERO_RS19360
         (391 letters)



>lcl|FitnessBrowser__Smeli:SMa0247 SMa0247 hypothetical protein
          Length = 398

 Score =  439 bits (1129), Expect = e-128
 Identities = 229/387 (59%), Positives = 281/387 (72%), Gaps = 9/387 (2%)

Query: 6   SLQAHLPEDHAQATLIGRIWQPGVG-PVLVRIDADGAYDLTLIAATSSELLELDNPAAAV 64
           S ++  P D + A L+GR+W    G P  V I     +DLT +AAT S LLE+D    A+
Sbjct: 14  SAESIQPADASSAMLVGRVWSKTAGGPCPVLISEGEVFDLTPLAATISALLEIDGLVDAL 73

Query: 65  RSATNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEEQA 124
           R  +    + +L   L     AG       LLAP DLQAVKA+GVTF  SMLERVIEEQA
Sbjct: 74  RDPSRFASLGSLDAFLRGE--AGD------LLAPADLQAVKAAGVTFADSMLERVIEEQA 125

Query: 125 RGDAGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAEIF 184
           +GD  +A+ +R  +  V+GDNL  +V GS +AA +K++L + G+WSQYLEVGIGPDAEIF
Sbjct: 126 KGDPLRAQEIRGRLAPVLGDNLKGLVAGSDKAAEVKKLLQELGLWSQYLEVGIGPDAEIF 185

Query: 185 TKAQPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRSAL 244
           TKAQPMSSVG G  +GIHPKS WNNPEPE+VLA+ S+GK+VGATLGNDVNLRDFEGRSAL
Sbjct: 186 TKAQPMSSVGCGAYIGIHPKSDWNNPEPEVVLAVTSKGKIVGATLGNDVNLRDFEGRSAL 245

Query: 245 LLGKAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMISRDP 304
           LL KAKDNNASC++GPFIRLFD  F+I+DV++AE+++ VDG EGF + G S MS ISR P
Sbjct: 246 LLSKAKDNNASCSIGPFIRLFDGAFTIEDVKQAEVSLVVDGKEGFKMTGISPMSAISRSP 305

Query: 305 LQLVEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGALVNT 364
             LV   +  NHQYPDG+V FLGTMFAP +DR G G GFTH++ D V ISTP+LG LVN 
Sbjct: 306 EDLVSQLLNDNHQYPDGVVFFLGTMFAPVKDRRGTGLGFTHEIGDRVEISTPRLGRLVNW 365

Query: 365 VNFSDQTAPWTFGLTALFKNLADRKLI 391
           V+ SD+   W+FGL AL KNLA+R L+
Sbjct: 366 VDHSDRCPKWSFGLGALMKNLAERGLL 392


Lambda     K      H
   0.317    0.134    0.387 

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: 480
Number of extensions: 22
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: 391
Length of database: 398
Length adjustment: 31
Effective length of query: 360
Effective length of database: 367
Effective search space:   132120
Effective search space used:   132120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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