Alignments for a candidate for mal in Mesorhizobium ciceri biovar biserrulae WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for mal in Mesorhizobium ciceri biovar biserrulae WSM1271

Align Methylaspartate ammonia-lyase 1; MAL; 3-methylaspartate ammonia-lyase 1; Beta-methylaspartase 1; EC 4.3.1.2 (characterized)
to candidate WP_013533413.1 MESCI_RS28465 methylaspartate ammonia-lyase

Query= SwissProt::Q3AEU2
         (420 letters)



>NCBI__GCF_000185905.1:WP_013533413.1
          Length = 417

 Score =  347 bits (891), Expect = e-100
 Identities = 185/414 (44%), Positives = 251/414 (60%), Gaps = 4/414 (0%)

Query: 1   MRIKDVLFVKGSSGFYFDDQKAIKSGAVTDGFTYKGKPLTPGFSRVRQGGEAVSIMLFLE 60
           M+IKDVL   G+  F++DDQ+AI+SGA+ DGF Y G P TPGF  +R    ++SI L L 
Sbjct: 1   MQIKDVLLAPGNGAFFYDDQEAIRSGAIQDGFMYVGAPTTPGFKSIRIPASSLSIGLVLA 60

Query: 61  NGEIAVGDCVAVQYSGVDGRDPVFLADNFIEVLEEEIKPRLVGYNLVRFREAA-RYFTNL 119
           +  +  GD + VQY+G  GRDP+F  +   ++    + PRL   +  RF ++  R F ++
Sbjct: 61  DETVVWGDMMNVQYAGAGGRDPLFDTNQISDLTSCVVAPRLFDVDASRFIDSCTRVFESV 120

Query: 120 TDKRGKRYHTALRYGLTQALLDAVAKINRTTMAEVIAEEYGLDLTLNPVPLFAQSGDDRY 179
              R      A+ YG++QALL A A + R TMAE++  E+ L L    VP++ QSGD R 
Sbjct: 121 EHLR---IPLAIEYGVSQALLRAAAHLQRKTMAEIVCAEFDLPLPTCRVPIYCQSGDARE 177

Query: 180 INADKMILKRVDVLPHGLFNHPAKTGEEGKNLTEYALWLKQRIKTLGDHDYLPVFHFDVY 239
           IN D+MILK VD+LPHGL N   K G +G+   ++  W+  R + +G   Y PV HFDVY
Sbjct: 178 INVDRMILKGVDILPHGLINSRQKFGTDGQTFMDFVKWVATRTRQIGLPGYHPVLHFDVY 237

Query: 240 GTLGTVFNDNLDRIADYLARLEEKVAPHPLQIEGPVDLGSKERQIEGLKYLQEKLITLGS 299
           G +G        RIAD++ R+ E V    L +E P D GS + QIE    +   L   GS
Sbjct: 238 GWIGLEIGLEPQRIADFICRVAESVPGFALNVESPADFGSTQAQIENYAEIVSILDNRGS 297

Query: 300 KVIIVADEWCNNLSDIKEFVDAGAGGMVQIKSPDLGGVNDIIEAVLYAKEKGTGAYLGGS 359
           +  IV DE CN L DI+ F +A A  +VQIK+PD+G + D   AVL  KE   GAY+GGS
Sbjct: 298 RARIVVDERCNTLEDIRLFAEAKATHLVQIKTPDVGSIADTARAVLICKENRVGAYVGGS 357

Query: 360 CNETDVSAKITVHVGLATGPAQLLVKPGMGVDEGLTIMRNEMMRTLAILQRNKV 413
           C ETD+SA+ +VH+ +AT    +L KPGMGVDEG +I+ NE  R LAIL R +V
Sbjct: 358 CTETDLSAQASVHISVATQADMMLAKPGMGVDEGFSIVGNEQNRLLAILNRRRV 411


Lambda     K      H
   0.319    0.139    0.404 

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: 435
Number of extensions: 17
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: 420
Length of database: 417
Length adjustment: 32
Effective length of query: 388
Effective length of database: 385
Effective search space:   149380
Effective search space used:   149380
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: 50 (23.9 bits)

Align candidate WP_013533413.1 MESCI_RS28465 (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.831878.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-206  671.1   0.0   3.5e-206  670.9   0.0    1.0  1  NCBI__GCF_000185905.1:WP_013533413.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000185905.1:WP_013533413.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  670.9   0.0  3.5e-206  3.5e-206       1     408 []       2     409 ..       2     409 .. 1.00

  Alignments for each domain:
  == domain 1  score: 670.9 bits;  conditional E-value: 3.5e-206
                             TIGR01502   1 kikdvlltPGvagfffddqaaikaGadadGlvyvGspategferirekgeslsvelvledgrvvrGdcaavqy 73 
                                           +ikdvll+PG ++ff+ddq ai+ Ga +dG++yvG p+t+gf++ir ++ sls++lvl d++vv+Gd++ vqy
  NCBI__GCF_000185905.1:WP_013533413.1   2 QIKDVLLAPGNGAFFYDDQEAIRSGAIQDGFMYVGAPTTPGFKSIRIPASSLSIGLVLADETVVWGDMMNVQY 74 
                                           79*********************************************************************** PP

                             TIGR01502  74 sGaGgrdplfeakdisavvekavaekligrdvarvkda.akvfekladernlhtairyGvsqallaaaakark 145
                                           +GaGgrdplf +++is++++ +va++l ++d++r+ d+ ++vfe++ + r +++ai+yGvsqall+aaa++++
  NCBI__GCF_000185905.1:WP_013533413.1  75 AGAGGRDPLFDTNQISDLTSCVVAPRLFDVDASRFIDScTRVFESVEHLR-IPLAIEYGVSQALLRAAAHLQR 146
                                           *************************************9899*********.********************** PP

                             TIGR01502 146 ttmaevvadeldleleteavPvfaqsGddrernvdkmilkevdvlPhglinsveklGldGeklleyvkwlser 218
                                            tmae+v+ e+dl+l+t +vP+++qsGd+re nvd+milk vd+lPhglins++k+G dG++++++vkw+++r
  NCBI__GCF_000185905.1:WP_013533413.1 147 KTMAEIVCAEFDLPLPTCRVPIYCQSGDAREINVDRMILKGVDILPHGLINSRQKFGTDGQTFMDFVKWVATR 219
                                           ************************************************************************* PP

                             TIGR01502 219 iaklgsegyrPvlhvdvyGliGeefgldrkavadyirelaeaakpftlriegPmdvgsrqaqieamaelrael 291
                                           ++++g +gy+Pvlh+dvyG+iG e+gl+++++ad+i+++ae+++ f l++e+P+d+gs+qaqie++ae++++l
  NCBI__GCF_000185905.1:WP_013533413.1 220 TRQIGLPGYHPVLHFDVYGWIGLEIGLEPQRIADFICRVAESVPGFALNVESPADFGSTQAQIENYAEIVSIL 292
                                           ************************************************************************* PP

                             TIGR01502 292 ddrGvaaeivadewcntvedvklfvdakaadlvqiktPdvGgvaesaravlyckandvgayvGGtcnetdlsa 364
                                           d+rG+ a+iv+de+cnt+ed++lf++aka++lvqiktPdvG++a++aravl+ck n vgayvGG+c+etdlsa
  NCBI__GCF_000185905.1:WP_013533413.1 293 DNRGSRARIVVDERCNTLEDIRLFAEAKATHLVQIKTPDVGSIADTARAVLICKENRVGAYVGGSCTETDLSA 365
                                           ************************************************************************* PP

                             TIGR01502 365 easvhvalatdaaqvlakPGmGvdegfaivknemnrvlallrrr 408
                                           +asvh+++at+a+++lakPGmGvdegf+iv+ne+nr+la+l+rr
  NCBI__GCF_000185905.1:WP_013533413.1 366 QASVHISVATQADMMLAKPGMGVDEGFSIVGNEQNRLLAILNRR 409
                                           *****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (408 nodes)
Target sequences:                          1  (417 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.32
//
[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:

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