GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Rhodobacter viridis JA737

Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_110804852.1 C8J30_RS06230 lysine-2,3-aminomutase-like protein

Query= SwissProt::Q8RHX4
         (425 letters)



>NCBI__GCF_003217355.1:WP_110804852.1
          Length = 350

 Score =  259 bits (661), Expect = 1e-73
 Identities = 139/351 (39%), Positives = 206/351 (58%), Gaps = 7/351 (1%)

Query: 23  TWQVKNRLESVEDLKKYVDLSEEETEGVVRTLETLRMAITPYYFSLIDLNSDRCPIRKQA 82
           T  VK  L   EDL     ++  +   + +  +  R+ +TP   + I    D  P+  Q 
Sbjct: 2   TAPVKTALTCPEDLLAEGLIAPADMPALEQVAQDFRIRVTPAMRAAITAPQD--PVAAQF 59

Query: 83  IPTIQEIHQSDADLLDPLHEDEDSPVPGLTHRYPDRVLLLITDMCSMYCRHCTRRRFAGS 142
           +PT  E+     +  DP+ +   SP PGLTHRYPDR +L IT  C +YCR C RR   G 
Sbjct: 60  VPTAAELITRPEERADPIGDAVHSPAPGLTHRYPDRAILHITKTCDVYCRFCFRRETVGE 119

Query: 143 SDDAMPMDRIDKAIEYIAKTPQVRDVLLSGGDALLVSDKKLESIIQKLRAIPHVEIIRIG 202
           +   +P   + +A+ YIA T  +R+++L+GGD L +S ++LE ++ +L AIPH+  +R+ 
Sbjct: 120 TGP-LPEADLAQALAYIAATRGLREIILTGGDPLTLSPRRLEDVLTRLSAIPHITTLRVH 178

Query: 203 SRTPVVLPQRITPELCNMLKKYHP-IWLNTHFNHPQEVTPEAKKACEMLADAGVPLGNQT 261
           SR PVV P+RITP L ++L+   P +W+  H NH QE+T  A+ A   L +AGVPL +Q+
Sbjct: 179 SRVPVVAPERITPALVDLLRGQRPAVWVVVHTNHAQELTAPARAALARLVEAGVPLLSQS 238

Query: 262 VLLRGINDSVPVMKRLVHDLVMMRVRPYYIYQCDLSMGLEHFRTPVSKGIEIIEGLRGHT 321
           VLLRG+NDS   +  L   L   RV+PYY++ CDL+ G   FRT ++ G  ++ GLRGH 
Sbjct: 239 VLLRGVNDSHQALVDLFRALQDCRVKPYYLHHCDLAPGTSQFRTTIAAGRALVAGLRGHL 298

Query: 322 SGYAVPTFVVDAPGGGGKTPVMPQYVISQSPHRVVLR--NFEGVITTYTEP 370
           SG A+PT+V+D PGG GK P+   +  S  P     R  +++G +  Y +P
Sbjct: 299 SGAAIPTYVLDIPGGFGKVPITADH-FSPGPRPGTWRVTDWQGGLHDYADP 348


Lambda     K      H
   0.319    0.137    0.411 

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: 432
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: 425
Length of database: 350
Length adjustment: 30
Effective length of query: 395
Effective length of database: 320
Effective search space:   126400
Effective search space used:   126400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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