GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Desulfoscipio geothermicus DSM 3669

Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_092483144.1 BM299_RS08870 glutamate 2,3-aminomutase

Query= SwissProt::Q9XBQ8
         (416 letters)



>NCBI__GCF_900115975.1:WP_092483144.1
          Length = 413

 Score =  388 bits (996), Expect = e-112
 Identities = 184/361 (50%), Positives = 259/361 (71%), Gaps = 3/361 (0%)

Query: 4   RRYEL--FKDVSDADWNDWRWQVRNRIETVEELKKYIPLTKEEEEGVAQCVKSLRMAITP 61
           R+ EL  F   ++ +W DW WQ+RNRI  V  L+K   LT+EE E +    +  R A++P
Sbjct: 46  RKKELLQFFGATEENWQDWHWQMRNRISDVGMLRKLWSLTEEEAEQIESVSEKFRWAVSP 105

Query: 62  YYLSLIDPNDPNDPVRKQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLI 121
           YYLSL++P +P  PVR Q IP+  EL      L DP+ E+  SP P +T RY DR+++ +
Sbjct: 106 YYLSLMEPGNPGCPVRMQGIPSIRELQDNWGKL-DPMAEEYTSPAPRITRRYADRLIINV 164

Query: 122 TDMCSMYCRHCTRRRFAGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETL 181
           T+ C+M+CRHC RRR  G+ D   P+E I  AIDYIR  P+VRDVL++GGD L +SDE L
Sbjct: 165 TNQCAMFCRHCQRRRSIGEVDKPAPVEEIKAAIDYIRQNPEVRDVLITGGDPLTLSDEWL 224

Query: 182 EYIIAKLREIPHVEIVRIGSRTPVVLPQRITPELVNMLKKYHPVWLNTHFNHPNEITEES 241
           ++I+++L +I HVEI RIGSRTPV +PQRITPEL  ML+ +HP++LNTHFNHP E+T+E+
Sbjct: 225 DWILSELDKIEHVEIKRIGSRTPVTMPQRITPELCAMLESHHPLYLNTHFNHPREVTQEA 284

Query: 242 TRACQLLADAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHF 301
            RA ++LA AG+ LGNQ+VLL+G+N+  HVMK+L ++L+KI VRPYYI+      G  HF
Sbjct: 285 LRATRMLAKAGISLGNQAVLLKGINNDPHVMKKLNHELLKIHVRPYYIFHAKPVKGTTHF 344

Query: 302 RTPVSKGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKTPVMPNYVISQSHDKVILRNFEGV 361
            T V +G+EI+E LRG+TSG  +P ++++APGG GKTP++P Y+++   D V++R +EG 
Sbjct: 345 VTTVQEGLEIMENLRGYTSGLAIPWYIINAPGGAGKTPLLPQYLLTMGKDYVMIRTWEGK 404

Query: 362 I 362
           +
Sbjct: 405 V 405


Lambda     K      H
   0.320    0.138    0.422 

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: 498
Number of extensions: 14
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: 416
Length of database: 413
Length adjustment: 31
Effective length of query: 385
Effective length of database: 382
Effective search space:   147070
Effective search space used:   147070
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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