Alignments for a candidate for dsdA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for dsdA in Klebsiella michiganensis M5al

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate BWI76_RS27860 BWI76_RS27860 D-serine dehydratase

Query= BRENDA::P00926
         (442 letters)



>FitnessBrowser__Koxy:BWI76_RS27860
          Length = 442

 Score =  789 bits (2037), Expect = 0.0
 Identities = 384/442 (86%), Positives = 417/442 (94%)

Query: 1   MENAKMNSLIAQYPLVKDLVALKETTWFNPGTTSLAEGLPYVGLTEQDVQDAHARLSRFA 60
           M+NA M +L+AQ+PL+++L+ALKETTWFNP TTSLAEGLPYVGLT +DVQDAHARL RFA
Sbjct: 1   MKNADMTTLLAQFPLLEELIALKETTWFNPSTTSLAEGLPYVGLTTEDVQDAHARLDRFA 60

Query: 61  PYLAKAFPETAATGGIIESELVAIPAMQKRLEKEYQQPISGQLLLKKDSHLPISGSIKAR 120
           PYLA+AFPETAATGGIIESELVAIP M+  LEK + QPISG LLLKKDSHLPISGSIKAR
Sbjct: 61  PYLAEAFPETAATGGIIESELVAIPVMKAWLEKTFSQPISGDLLLKKDSHLPISGSIKAR 120

Query: 121 GGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSA 180
           GGIYEVL HAEKLA+ AGLL   DDY KLL+PEF+ FFSQYSIAVGSTGNLG+SIGIMSA
Sbjct: 121 GGIYEVLTHAEKLAIGAGLLKTSDDYRKLLTPEFRDFFSQYSIAVGSTGNLGMSIGIMSA 180

Query: 181 RIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDEN 240
           RIGFKVTVHMSADARAWKKAKLRSHGVTVVEYE+DYGVAVE+GRKAA+SDPNCFFIDDEN
Sbjct: 181 RIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEEDYGVAVEQGRKAAESDPNCFFIDDEN 240

Query: 241 SRTLFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVH 300
           SRTLFLGY+VAG+RLKAQFA++ R+VDA +PLFVYLPCGVGGGPGGVAFGLKLAFGDHVH
Sbjct: 241 SRTLFLGYAVAGERLKAQFAREARVVDAGHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVH 300

Query: 301 CFFAEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGF 360
           C FAEPTHSPCMLLGV+TGLHDQISVQD+GIDNLTAADGLAVGRASGFVGRAMERLLDGF
Sbjct: 301 CLFAEPTHSPCMLLGVYTGLHDQISVQDLGIDNLTAADGLAVGRASGFVGRAMERLLDGF 360

Query: 361 YTLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCASVSYQQMHGFSAEQLRNTTHL 420
           Y+L DQTMYDMLGWLA+EEGIRLEPSALAGMAGPQRVCAS +YQ+MHGF+AEQ+RN THL
Sbjct: 361 YSLDDQTMYDMLGWLAEEEGIRLEPSALAGMAGPQRVCASEAYQRMHGFTAEQMRNATHL 420

Query: 421 VWATGGGMVPEEEMNQYLAKGR 442
           VWATGGGMVPEEEM QYLAKGR
Sbjct: 421 VWATGGGMVPEEEMAQYLAKGR 442


Lambda     K      H
   0.319    0.135    0.399 

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: 739
Number of extensions: 12
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: 442
Length of database: 442
Length adjustment: 32
Effective length of query: 410
Effective length of database: 410
Effective search space:   168100
Effective search space used:   168100
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 BWI76_RS27860 BWI76_RS27860 (D-serine dehydratase)
to HMM TIGR02035 (dsdA: D-serine ammonia-lyase (EC 4.3.1.18))

# 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/TIGR02035.hmm
# target sequence database:        /tmp/gapView.2023.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02035  [M=431]
Accession:   TIGR02035
Description: D_Ser_am_lyase: D-serine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.1e-237  773.8   0.0   2.4e-237  773.7   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27860  BWI76_RS27860 D-serine dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27860  BWI76_RS27860 D-serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  773.7   0.0  2.4e-237  2.4e-237       2     431 .]      10     438 ..       9     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 773.7 bits;  conditional E-value: 2.4e-237
                               TIGR02035   2 llkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiiese 72 
                                             l+++pl+++li+lke++w+np+++slae l++v+l+ ++v++a+arl+rfapy+a++fpetaat+Giiese
  lcl|FitnessBrowser__Koxy:BWI76_RS27860  10 LAQFPLLEELIALKETTWFNPSTTSLAEGLPYVGLTTEDVQDAHARLDRFAPYLAEAFPETAATGGIIESE 80 
                                             899******************************************************************** PP

                               TIGR02035  73 lvevaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllkldddysklae 143
                                             lv++  +k  lek++ q++sG lllkkdshlpisGsikarGGiyevl haekla+ aGllk  ddy+kl+ 
  lcl|FitnessBrowser__Koxy:BWI76_RS27860  81 LVAIPVMKAWLEKTFSQPISGDLLLKKDSHLPISGSIKARGGIYEVLTHAEKLAIGAGLLKTSDDYRKLLT 151
                                             *********************************************************************** PP

                               TIGR02035 144 eefkdffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdyskavee 214
                                             +ef+dffs+y+iavGstGnlG+siGi+sa++Gfkvtvhmsada++wkk+klrs+Gvtvveye+dy++ave+
  lcl|FitnessBrowser__Koxy:BWI76_RS27860 152 PEFRDFFSQYSIAVGSTGNLGMSIGIMSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEEDYGVAVEQ 222
                                             *********************************************************************** PP

                               TIGR02035 215 GrkeaeadplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGGvafGlkl 285
                                             Grk+ae+dp+++f+dde+sr+lflGyava++rlk+q+++++++vd+ hplfvylpcGvGGgpGGvafGlkl
  lcl|FitnessBrowser__Koxy:BWI76_RS27860 223 GRKAAESDPNCFFIDDENSRTLFLGYAVAGERLKAQFAREARVVDAGHPLFVYLPCGVGGGPGGVAFGLKL 293
                                             *********************************************************************** PP

                               TIGR02035 286 lfgddvhvffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGlvGrllerlldGiytvd 356
                                             +fgd+vh++faepthspcmllG+ytGlh++isvqd+GidnltaadGlavgr+sG+vGr++erlldG+y++d
  lcl|FitnessBrowser__Koxy:BWI76_RS27860 294 AFGDHVHCLFAEPTHSPCMLLGVYTGLHDQISVQDLGIDNLTAADGLAVGRASGFVGRAMERLLDGFYSLD 364
                                             *********************************************************************** PP

                               TIGR02035 357 deklydllallaesedkrlepsalaglaGvvrllkeeeskreaekliakklenavhlvwatGGkmvpeeem 427
                                             d+++yd+l +lae+e++rlepsalag+aG++r++++ e+++++++++a++++na+hlvwatGG+mvpeeem
  lcl|FitnessBrowser__Koxy:BWI76_RS27860 365 DQTMYDMLGWLAEEEGIRLEPSALAGMAGPQRVCAS-EAYQRMHGFTAEQMRNATHLVWATGGGMVPEEEM 434
                                             ***********************************9.89******************************** PP

                               TIGR02035 428 eayl 431
                                             ++yl
  lcl|FitnessBrowser__Koxy:BWI76_RS27860 435 AQYL 438
                                             **96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (442 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.16
//
[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