Alignments for a candidate for kamA in Methanospirillum stamsii Pt1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kamA in Methanospirillum stamsii Pt1

Align lysine 2,3-aminomutase (EC 5.4.3.2) (characterized)
to candidate WP_109941996.1 DLD82_RS15265 lysine 2,3-aminomutase

Query= BRENDA::G3F9W8
         (439 letters)



>NCBI__GCF_003173335.1:WP_109941996.1
          Length = 437

 Score =  579 bits (1492), Expect = e-170
 Identities = 277/426 (65%), Positives = 337/426 (79%), Gaps = 7/426 (1%)

Query: 17  IGEDAPQWRDWRWQIAHTVRSLSMLEKVLGITFPPEEREKLQETIDKFPLAATPYYLSLI 76
           + ++  +W+DW+WQ+ H++  ++ LE+ LG+     ERE + +T D FP++ TPYYLSLI
Sbjct: 15  VQQNNAKWKDWKWQVGHSITDITTLEQTLGMNLSKSEREDMIKTCDIFPMSITPYYLSLI 74

Query: 77  KTEDYANDPIFRQAVPVPDELRVEECELEDPLAEDSDSPVPGITHRYPDRVLFLVSNVCA 136
            T+D  +DPIFRQAVP P EL +E  +L DPL+ED+DSP P ITHRYPDRVLFL+SN CA
Sbjct: 75  NTDDPLHDPIFRQAVPSPGELIIENYDLHDPLSEDADSPCPLITHRYPDRVLFLISNTCA 134

Query: 137 MYCRHCTRKRKVGDRDRIPTWEEMEVGITYIREHPEVRDVLLSGGDPLMLPDDLLDRILT 196
           MYCRHCTRKRKVG     P  EE++   +YI  H E+RDVLLSGGDPLML D  LD IL 
Sbjct: 135 MYCRHCTRKRKVGQVLSAPLKEELDEAFSYIETHSEIRDVLLSGGDPLMLSDKELDTILR 194

Query: 197 QLRAIPHVEVIRIGSRTPVVLPFRITDGLVNVLKKHQPIWLNTHFNHPQEITPSAEKALA 256
           +LR IPHVE+IRIGSR PVVLPFRITD LV++LKK+ P+WLNTHFNHP E T  + +ALA
Sbjct: 195 RLRKIPHVEIIRIGSRVPVVLPFRITDNLVSILKKYHPLWLNTHFNHPHEFTTESCEALA 254

Query: 257 KLADAGIPLGNQSVLLAGVNDCPRIMKSLVQKLVKNRVRPYYLYQCDLSEGLSHFRTPVG 316
           KLADAGIPLGNQSVLLAGVNDCP IM+ LV +LVKNRVRPYYL+QCDL+EGL+HFRTPVG
Sbjct: 255 KLADAGIPLGNQSVLLAGVNDCPEIMRKLVHELVKNRVRPYYLFQCDLAEGLAHFRTPVG 314

Query: 317 KGIEIMENLIGHTSGFAVPTYVIDAPGGGGKIPVMPTYLISYSTNKVILRNFEGVITTYR 376
           KGIEI+E+LIGHTSG AVPTYVIDAPGGGGKIPVMP YL+S+S+NKV+LRN+EG+ TTY+
Sbjct: 315 KGIEIIESLIGHTSGLAVPTYVIDAPGGGGKIPVMPYYLVSWSSNKVVLRNYEGMFTTYQ 374

Query: 377 EPDNYTSIFCDRNCKDCSLQLKLEAGDEQHVV----GIAKLLSDYDEATALVPADSERMA 432
           EPDNY  I CD NC+ C LQ      D++ +V    GI  LLSDY+ +  ++PA   R+A
Sbjct: 375 EPDNYQGITCDLNCEKCRLQ---HIEDQETMVKRAQGIEALLSDYENSITILPAVLNRIA 431

Query: 433 RREDEE 438
           RR+D E
Sbjct: 432 RRQDGE 437


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: 648
Number of extensions: 24
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: 439
Length of database: 437
Length adjustment: 32
Effective length of query: 407
Effective length of database: 405
Effective search space:   164835
Effective search space used:   164835
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_109941996.1 DLD82_RS15265 (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.466167.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-215  701.4   0.1     2e-215  701.2   0.1    1.0  1  NCBI__GCF_003173335.1:WP_109941996.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003173335.1:WP_109941996.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  701.2   0.1    2e-215    2e-215       3     417 .]      18     433 ..      16     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 701.2 bits;  conditional E-value: 2e-215
                             TIGR03820   3 seeewkdwkwqlrnsikdvdtlekllgiklseeekeelketvekfplsitpyylslidaedlendpiflqsvp 75 
                                           ++ +wkdwkwq+ +si+d+ tle+ lg++ls++e+e++ +t + fp+sitpyylsli+++d  +dpif+q+vp
  NCBI__GCF_003173335.1:WP_109941996.1  18 NNAKWKDWKWQVGHSITDITTLEQTLGMNLSKSEREDMIKTCDIFPMSITPYYLSLINTDDPLHDPIFRQAVP 90 
                                           6789********************************************************************* PP

                             TIGR03820  76 sskelevesadledplaedkdspvegithrypdrvlflvsntcamycrhctrkrkvgdkdsipskeeikegie 148
                                           s+ el++e++dl+dpl+ed+dsp++ ithrypdrvlfl+sntcamycrhctrkrkvg++ s+p kee++e+  
  NCBI__GCF_003173335.1:WP_109941996.1  91 SPGELIIENYDLHDPLSEDADSPCPLITHRYPDRVLFLISNTCAMYCRHCTRKRKVGQVLSAPLKEELDEAFS 163
                                           ************************************************************************* PP

                             TIGR03820 149 yiretpqvrdvllsGGdplllsdelldwilselkaiehveviriGtrvpvvlpyritdelveilkkyhpvwln 221
                                           yi+ ++++rdvllsGGdpl+lsd+ ld il  l++i+hve+iriG+rvpvvlp+ritd+lv+ilkkyhp+wln
  NCBI__GCF_003173335.1:WP_109941996.1 164 YIETHSEIRDVLLSGGDPLMLSDKELDTILRRLRKIPHVEIIRIGSRVPVVLPFRITDNLVSILKKYHPLWLN 236
                                           ************************************************************************* PP

                             TIGR03820 222 thfnhpkeitksskkalakladaGiplGnqsvllagvndcprilkklvhklvknrvrpyylyqcdlseGlshf 294
                                           thfnhp+e t++s +alakladaGiplGnqsvllagvndcp+i++klvh+lvknrvrpyyl+qcdl+eGl+hf
  NCBI__GCF_003173335.1:WP_109941996.1 237 THFNHPHEFTTESCEALAKLADAGIPLGNQSVLLAGVNDCPEIMRKLVHELVKNRVRPYYLFQCDLAEGLAHF 309
                                           ************************************************************************* PP

                             TIGR03820 295 rtpvskGieilesliGhtsGfavptyvvdapgGGGkipvmpnylisqstnkvvlrnyeGvittykepdsyeea 367
                                           rtpv+kGiei+esliGhtsG+avptyv+dapgGGGkipvmp yl+s+s+nkvvlrnyeG+ tty+epd+y+ +
  NCBI__GCF_003173335.1:WP_109941996.1 310 RTPVGKGIEIIESLIGHTSGLAVPTYVIDAPGGGGKIPVMPYYLVSWSSNKVVLRNYEGMFTTYQEPDNYQGI 382
                                           ************************************************************************* PP

                             TIGR03820 368 lcdrkcekcelkl.kledaeeskavGieklladeddtislvpeenerlerr 417
                                           +cd +cekc+l+  + +++  ++a Gie ll+d++++i+++p   +r++rr
  NCBI__GCF_003173335.1:WP_109941996.1 383 TCDLNCEKCRLQHiEDQETMVKRAQGIEALLSDYENSITILPAVLNRIARR 433
                                           *********9875155566778999**********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (437 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.68
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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