GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kamA in Chlorobaculum parvum NCIB 8327

Align lysine 2,3-aminomutase (EC 5.4.3.2) (characterized)
to candidate WP_012502633.1 CPAR_RS07105 lysine 2,3-aminomutase

Query= BRENDA::G3F9X2
         (437 letters)



>NCBI__GCF_000020505.1:WP_012502633.1
          Length = 440

 Score =  639 bits (1647), Expect = 0.0
 Identities = 296/431 (68%), Positives = 351/431 (81%)

Query: 7   AQKEIAKKIDSDTVIANWKDWRWQLKHSIGDIDTFETLLGIKFKPGEKDKLKQTLEKFPL 66
           AQK+I K+ID +T  ++W DWRWQ++HSI D+DTFE LL I     ++    +T++KFP+
Sbjct: 6   AQKQIIKRIDPETTPSDWSDWRWQMRHSIRDLDTFERLLDITLSDEQRKAFGETVQKFPM 65

Query: 67  SVTPYYLSLIDAEDFRNDPIFLQAFPSPKELDIDEDDLEDPLSEDEDSPVEGITHRYPDR 126
           S TPYYLSLI+ +D  NDP+FLQ+ PSP EL I + D+ DPL EDEDSP   +THRYPDR
Sbjct: 66  STTPYYLSLINTDDMENDPVFLQSVPSPLELKIMKGDMADPLHEDEDSPAPCVTHRYPDR 125

Query: 127 VLFHISNTCSMYCRHCTRKRKVGDVDSIPTKDAVSEGLEYIRNTPQVRDVLLSGGDPFML 186
           VL  +SNTC MYCRHCTRKRKVGD D+IP + A+  G++YIRNTPQVRDVLLSGGDPF+L
Sbjct: 126 VLLLVSNTCPMYCRHCTRKRKVGDEDTIPNRAAIQAGIDYIRNTPQVRDVLLSGGDPFLL 185

Query: 187 PDAYLDWILAKLREIPHVEIIRIGTRMPVVLPYRVTDDLVKILKKHHPLWINTHFNHPRE 246
            D  LDWIL +LR I HVEIIR+GTR PVVLP R+T +LV IL KH P+W+NTHFNHPRE
Sbjct: 186 SDEMLDWILTELRAIEHVEIIRVGTRTPVVLPQRITPELVAILGKHQPVWVNTHFNHPRE 245

Query: 247 VTASSREALRKLADAGIPLGNQTVLLSGVNDCHRIMKRLVQKLVQNRVRPYYLYQCDLSE 306
           +T S+R AL +LAD G+PLGNQTVLLSG+NDC RIMK LV KLV NRVRPYYLYQCDLSE
Sbjct: 246 MTQSARNALARLADVGVPLGNQTVLLSGINDCPRIMKALVHKLVANRVRPYYLYQCDLSE 305

Query: 307 GLSHFRTPVGKGIEIMEHLIGHTSGFAVPTYVIDAPHGGGKIPVMPSYLISWSTNRVILR 366
           GLSHFRTPVGKGIEI+E LIGHTSGF VPTYVIDAP GGGKIPVMP+YLISWSTN+V+LR
Sbjct: 306 GLSHFRTPVGKGIEILESLIGHTSGFCVPTYVIDAPGGGGKIPVMPNYLISWSTNKVVLR 365

Query: 367 NYEGVITSYKEPDSYEPIYCDRKCEECKLQLKLDDAAEYKSTGIAKLLADNDEVVSLVPE 426
           NYEGVIT+YKEPDSYEP +CDR C EC LQL  +DA + K+ G+ +LLAD+D+ +SL+P 
Sbjct: 366 NYEGVITTYKEPDSYEPTFCDRNCTECDLQLNFEDAEQSKAIGVQQLLADHDQTISLIPS 425

Query: 427 DTERMERRDVE 437
              R +RR  E
Sbjct: 426 SNARHKRRKGE 436


Lambda     K      H
   0.319    0.138    0.420 

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: 651
Number of extensions: 21
Number of successful extensions: 1
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: 437
Length of database: 440
Length adjustment: 32
Effective length of query: 405
Effective length of database: 408
Effective search space:   165240
Effective search space used:   165240
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: 51 (24.3 bits)

Align candidate WP_012502633.1 CPAR_RS07105 (lysine 2,3-aminomutase)
to HMM TIGR03820 (ablA: lysine-2,3-aminomutase (EC 5.4.3.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03820.hmm
# target sequence database:        /tmp/gapView.453952.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03820  [M=417]
Accession:   TIGR03820
Description: lys_2_3_AblA: lysine-2,3-aminomutase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-239  779.4   0.0   4.2e-239  779.2   0.0    1.0  1  NCBI__GCF_000020505.1:WP_012502633.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020505.1:WP_012502633.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  779.2   0.0  4.2e-239  4.2e-239       3     417 .]      19     433 ..      17     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 779.2 bits;  conditional E-value: 4.2e-239
                             TIGR03820   3 seeewkdwkwqlrnsikdvdtlekllgiklseeekeelketvekfplsitpyylslidaedlendpiflqsvp 75 
                                           + ++w+dw+wq+r+si+d+dt+e+ll+i+ls+e+++++ etv+kfp+s tpyylsli+++d+endp+flqsvp
  NCBI__GCF_000020505.1:WP_012502633.1  19 TPSDWSDWRWQMRHSIRDLDTFERLLDITLSDEQRKAFGETVQKFPMSTTPYYLSLINTDDMENDPVFLQSVP 91 
                                           5689********************************************************************* PP

                             TIGR03820  76 sskelevesadledplaedkdspvegithrypdrvlflvsntcamycrhctrkrkvgdkdsipskeeikegie 148
                                           s+ el++++ d++dpl+ed+dsp++++thrypdrvl+lvsntc mycrhctrkrkvgd+d+ip++  i++gi+
  NCBI__GCF_000020505.1:WP_012502633.1  92 SPLELKIMKGDMADPLHEDEDSPAPCVTHRYPDRVLLLVSNTCPMYCRHCTRKRKVGDEDTIPNRAAIQAGID 164
                                           ************************************************************************* PP

                             TIGR03820 149 yiretpqvrdvllsGGdplllsdelldwilselkaiehveviriGtrvpvvlpyritdelveilkkyhpvwln 221
                                           yir+tpqvrdvllsGGdp+llsde+ldwil+el+aiehve+ir+Gtr+pvvlp+rit+elv+il k++pvw+n
  NCBI__GCF_000020505.1:WP_012502633.1 165 YIRNTPQVRDVLLSGGDPFLLSDEMLDWILTELRAIEHVEIIRVGTRTPVVLPQRITPELVAILGKHQPVWVN 237
                                           ************************************************************************* PP

                             TIGR03820 222 thfnhpkeitksskkalakladaGiplGnqsvllagvndcprilkklvhklvknrvrpyylyqcdlseGlshf 294
                                           thfnhp+e+t+s+++ala+lad+G+plGnq+vll+g+ndcpri+k+lvhklv+nrvrpyylyqcdlseGlshf
  NCBI__GCF_000020505.1:WP_012502633.1 238 THFNHPREMTQSARNALARLADVGVPLGNQTVLLSGINDCPRIMKALVHKLVANRVRPYYLYQCDLSEGLSHF 310
                                           ************************************************************************* PP

                             TIGR03820 295 rtpvskGieilesliGhtsGfavptyvvdapgGGGkipvmpnylisqstnkvvlrnyeGvittykepdsyeea 367
                                           rtpv+kGieilesliGhtsGf+vptyv+dapgGGGkipvmpnylis+stnkvvlrnyeGvittykepdsye++
  NCBI__GCF_000020505.1:WP_012502633.1 311 RTPVGKGIEILESLIGHTSGFCVPTYVIDAPGGGGKIPVMPNYLISWSTNKVVLRNYEGVITTYKEPDSYEPT 383
                                           ************************************************************************* PP

                             TIGR03820 368 lcdrkcekcelklkledaeeskavGieklladeddtislvpeenerlerr 417
                                           +cdr+c++c+l+l+ edae+ska+G+++llad+d+tisl+p++n r++rr
  NCBI__GCF_000020505.1:WP_012502633.1 384 FCDRNCTECDLQLNFEDAEQSKAIGVQQLLADHDQTISLIPSSNARHKRR 433
                                           ***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (440 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 25.39
//
[ok]

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