Alignments for a candidate for mal in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for mal in Klebsiella michiganensis M5al

Align Methylaspartate ammonia-lyase; MAL; 3-methylaspartate ammonia-lyase; Beta-methylaspartase; EC 4.3.1.2 (characterized)
to candidate BWI76_RS08475 BWI76_RS08475 methylaspartate ammonia-lyase

Query= SwissProt::O66145
         (413 letters)



>FitnessBrowser__Koxy:BWI76_RS08475
          Length = 413

 Score =  817 bits (2110), Expect = 0.0
 Identities = 400/413 (96%), Positives = 406/413 (98%)

Query: 1   MKIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTGDPVTPGFTSVRQAGECVSVQLILE 60
           MKIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTG PVTPGFTSVRQAGECVSVQLILE
Sbjct: 1   MKIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTGAPVTPGFTSVRQAGECVSVQLILE 60

Query: 61  NGAVAVGDCAAVQYSGAGGRDPLFLAEHFIPFLNDHIKPLLEGRDVDAFLPNARFFDKLR 120
           NGAVAVGDCAAVQYSGAGGRDPLFLAE+FIPFLNDHIKPLLEGRDVD FLPNARFFDKLR
Sbjct: 61  NGAVAVGDCAAVQYSGAGGRDPLFLAENFIPFLNDHIKPLLEGRDVDTFLPNARFFDKLR 120

Query: 121 IDGNLLHTAVRYGLSQALLDATALASGRLKTEVVCDEWQLPCVPEAIPLFGQSGDDRYIA 180
           IDG+LLHTAVRYGLSQALLDATALASGRLK EVVCDEWQLPC+PEAIPLFGQSGDDRYIA
Sbjct: 121 IDGHLLHTAVRYGLSQALLDATALASGRLKAEVVCDEWQLPCIPEAIPLFGQSGDDRYIA 180

Query: 181 VDKMILKGVDVLPHALINNVEEKLGFKGEKLREYVRWLSDRILSLRSSPRYHPTLHIDVY 240
           VDKMILKGVDVLPHALINNVEEKLG KGEKLREYVRWLSDRILSLR+SPRY PTLHIDVY
Sbjct: 181 VDKMILKGVDVLPHALINNVEEKLGLKGEKLREYVRWLSDRILSLRASPRYRPTLHIDVY 240

Query: 241 GTIGLIFDMDPVRCAEYIASLEKEAQGLPLYIEGPVDAGNKPDQIRMLTAITKELTRLGS 300
           GTIGLIFDMDPVRCA+YIASLEKEAQGLPLYIEGPVDAGNKPDQIRMLTAITKELTRLGS
Sbjct: 241 GTIGLIFDMDPVRCADYIASLEKEAQGLPLYIEGPVDAGNKPDQIRMLTAITKELTRLGS 300

Query: 301 GVKIVADEWCNTYQDIVDFTDAGSCHMVQIKTPDLGGIHNIVDAVLYCNKHGMEAYQGGT 360
           GVKIVADEWCNTYQDI+DFTDAGSCHMVQIKTPDLGGIHNIVDAVLYCNKH MEAYQGGT
Sbjct: 301 GVKIVADEWCNTYQDIIDFTDAGSCHMVQIKTPDLGGIHNIVDAVLYCNKHAMEAYQGGT 360

Query: 361 CNETEISARTCVHVALAARPMRMLIKPGMGFDEGLNIVFNEMNRTIALLQTKD 413
           CNETEISARTCVHVALAARPMRMLIKPGMGFDEGLNIVFNEMNRTIALLQ KD
Sbjct: 361 CNETEISARTCVHVALAARPMRMLIKPGMGFDEGLNIVFNEMNRTIALLQAKD 413


Lambda     K      H
   0.322    0.140    0.425 

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: 762
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: 413
Length of database: 413
Length adjustment: 31
Effective length of query: 382
Effective length of database: 382
Effective search space:   145924
Effective search space used:   145924
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS08475 BWI76_RS08475 (methylaspartate ammonia-lyase)
to HMM TIGR01502 (methylaspartate ammonia-lyase (EC 4.3.1.2))

# 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/TIGR01502.hmm
# target sequence database:        /tmp/gapView.8215.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01502  [M=408]
Accession:   TIGR01502
Description: B_methylAsp_ase: methylaspartate ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.6e-169  548.4   0.0   6.3e-169  548.2   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS08475  BWI76_RS08475 methylaspartate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS08475  BWI76_RS08475 methylaspartate ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.2   0.0  6.3e-169  6.3e-169       1     407 [.       2     411 ..       2     412 .. 0.99

  Alignments for each domain:
  == domain 1  score: 548.2 bits;  conditional E-value: 6.3e-169
                               TIGR01502   1 kikdvlltPGvagfffddqaaikaGadadGlvyvGspategferirekgeslsvelvledgrvvrGdcaav 71 
                                             kik+ l t G ++f+fddq+aik+Ga++dG++y+G p+t+gf+++r+ ge++sv+l+le+g v+ Gdcaav
  lcl|FitnessBrowser__Koxy:BWI76_RS08475   2 KIKQALFTAGYSSFYFDDQQAIKNGAGHDGFIYTGAPVTPGFTSVRQAGECVSVQLILENGAVAVGDCAAV 72 
                                             799******************************************************************** PP

                               TIGR01502  72 qysGaGgrdplfeakdisavvekavaekligrdvarvkdaakvfekladern.lhtairyGvsqallaaaa 141
                                             qysGaGgrdplf a+++++ ++  + + l grdv +++++a+ f+kl  ++  lhta+ryG+sqall+a+a
  lcl|FitnessBrowser__Koxy:BWI76_RS08475  73 QYSGAGGRDPLFLAENFIPFLNDHIKPLLEGRDVDTFLPNARFFDKLRIDGHlLHTAVRYGLSQALLDATA 143
                                             **************************************************9999***************** PP

                               TIGR01502 142 karkttmaevvadeldleleteavPvfaqsGddrernvdkmilkevdvlPhglinsvek.lGldGeklley 211
                                              a    +aevv+de++l+   ea+P+f+qsGddr+  vdkmilk vdvlPh+lin+ve+ lGl+Gekl ey
  lcl|FitnessBrowser__Koxy:BWI76_RS08475 144 LASGRLKAEVVCDEWQLPCIPEAIPLFGQSGDDRYIAVDKMILKGVDVLPHALINNVEEkLGLKGEKLREY 214
                                             *********************************************************988*********** PP

                               TIGR01502 212 vkwlseriaklg.segyrPvlhvdvyGliGeefgldrkavadyirelaeaakpftlriegPmdvgsrqaqi 281
                                             v+wls+ri  l+ s+ yrP lh+dvyG+iG  f++d+ + adyi  l + a+  +l iegP+d+g++  qi
  lcl|FitnessBrowser__Koxy:BWI76_RS08475 215 VRWLSDRILSLRaSPRYRPTLHIDVYGTIGLIFDMDPVRCADYIASLEKEAQGLPLYIEGPVDAGNKPDQI 285
                                             ************99********************************************************* PP

                               TIGR01502 282 eamaelraelddrGvaaeivadewcntvedvklfvdakaadlvqiktPdvGgvaesaravlyckandvgay 352
                                               ++ + +el   G+ ++ivadewcnt++d+  f+da+++++vqiktPd+Gg+ ++ +avlyc+   + ay
  lcl|FitnessBrowser__Koxy:BWI76_RS08475 286 RMLTAITKELTRLGSGVKIVADEWCNTYQDIIDFTDAGSCHMVQIKTPDLGGIHNIVDAVLYCNKHAMEAY 356
                                             *********************************************************************** PP

                               TIGR01502 353 vGGtcnetdlsaeasvhvalatdaaqvlakPGmGvdegfaivknemnrvlallrr 407
                                              GGtcnet++sa+++vhvala+   ++l kPGmG+deg+ iv nemnr++all++
  lcl|FitnessBrowser__Koxy:BWI76_RS08475 357 QGGTCNETEISARTCVHVALAARPMRMLIKPGMGFDEGLNIVFNEMNRTIALLQA 411
                                             ***************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (408 nodes)
Target sequences:                          1  (413 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: 00:00:00.01
# Mc/sec: 12.39
//
[ok]

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:

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 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