Alignments for a candidate for sdaB in Kocuria flava HO-9041

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Kocuria flava HO-9041

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_058857171.1 AS188_RS00370 L-serine ammonia-lyase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5557
         (458 letters)



>NCBI__GCF_001482365.1:WP_058857171.1
          Length = 477

 Score =  505 bits (1300), Expect = e-147
 Identities = 279/481 (58%), Positives = 332/481 (69%), Gaps = 27/481 (5%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60
           M++SVFDLF +GIGPSSSHTVGPMRAA RFA+ L   +L   T  ++V++YGSL ATG+G
Sbjct: 1   MAISVFDLFSVGIGPSSSHTVGPMRAARRFAQTLVEQELHERTAGLRVDVYGSLAATGRG 60

Query: 61  HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLA---MIR 117
           HG+  A+LLGLEG  P+TV  + V+ RL  I + G L L    ++   + L  A   M++
Sbjct: 61  HGTFTAILLGLEGYDPETVLPDQVEERLADIAAGGTLRLCA--ALGRRKDLPYAVEDMVQ 118

Query: 118 KPLAF---HPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGA--AGADRIVEDATPLTF 172
            PL     H NGM F+A DA G  +    ++SVGGGF+V EG   A A  + E +  +  
Sbjct: 119 HPLTVLERHTNGMRFQALDADGAVLADETWFSVGGGFIVQEGEEDAAAAELDEASKQVPH 178

Query: 173 PFKSAKDLLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGI 232
           PF++A++LL HC   GLSIS VML +E  WR E E RAGLL IW VM+ C  +  R  G 
Sbjct: 179 PFRTARELLAHCRATGLSISDVMLADERTWRTEEEIRAGLLHIWDVMEQCKDSSLRRTGT 238

Query: 233 LPGGLKVKRRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNG 292
           LPGGLKV RRA A H +L +  E   RDP    +WVNL ALAVNEENA GGRVVTAPTNG
Sbjct: 239 LPGGLKVARRAPAWHDRLRR--EDPDRDPSYWQEWVNLVALAVNEENASGGRVVTAPTNG 296

Query: 293 AAGIIPAVLHYYMRFIPGAS---------------EDGVVRFLLTAAAIGILYKENASIS 337
           AAGIIPAVL Y   ++P                  E  VVRFLL A A+G+LYKE ASIS
Sbjct: 297 AAGIIPAVLFYATHYVPEVRRAMAGGDAEELRRVRESVVVRFLLAAGAVGVLYKEQASIS 356

Query: 338 GAEVGCQGEVGVACSMAAGALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCI 397
           GAEVGCQGEVG A SMAAG L EVLGG+ +QVENAAEI MEHNLGLTCDPIGGLVQVPCI
Sbjct: 357 GAEVGCQGEVGSASSMAAGGLAEVLGGTPEQVENAAEIAMEHNLGLTCDPIGGLVQVPCI 416

Query: 398 ERNAMGSVKAINAVRMAMRGDGHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIE 457
           ERNA+ + KAINA +MA+ GDG H VSLD+VI TMR+TG DM  KYKETA GGLAVN++E
Sbjct: 417 ERNAIAAAKAINAAKMALWGDGTHRVSLDEVIVTMRETGKDMSHKYKETALGGLAVNVVE 476

Query: 458 C 458
           C
Sbjct: 477 C 477


Lambda     K      H
   0.320    0.136    0.401 

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: 701
Number of extensions: 29
Number of successful extensions: 5
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: 458
Length of database: 477
Length adjustment: 33
Effective length of query: 425
Effective length of database: 444
Effective search space:   188700
Effective search space used:   188700
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_058857171.1 AS188_RS00370 (L-serine ammonia-lyase)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

# 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/TIGR00720.hmm
# target sequence database:        /tmp/gapView.1968777.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00720  [M=450]
Accession:   TIGR00720
Description: sda_mono: L-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-200  652.4   0.0   2.7e-200  652.0   0.0    1.2  1  NCBI__GCF_001482365.1:WP_058857171.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001482365.1:WP_058857171.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  652.0   0.0  2.7e-200  2.7e-200       1     450 []       3     474 ..       3     474 .. 0.95

  Alignments for each domain:
  == domain 1  score: 652.0 bits;  conditional E-value: 2.7e-200
                             TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGel 73 
                                           isvfdlf++GiGPssshtvGPm+aa++f+++l +++  e+++ ++vd+yGsla+tG+Gh+t +a+llGleG++
  NCBI__GCF_001482365.1:WP_058857171.1   3 ISVFDLFSVGIGPSSSHTVGPMRAARRFAQTLVEQELHERTAGLRVDVYGSLAATGRGHGTFTAILLGLEGYD 75 
                                           79*********************************************************************** PP

                             TIGR00720  74 peevdiesieklleeveeekklkla....nqkeikfdlekdlafkdevlplhenglrlkaydeegevlkekty 142
                                           pe+v  +++e++l+++++ ++l+l     ++k++ + +e+ ++   +vl++h ng+r++a+d +g+vl+++t+
  NCBI__GCF_001482365.1:WP_058857171.1  76 PETVLPDQVEERLADIAAGGTLRLCaalgRRKDLPYAVEDMVQHPLTVLERHTNGMRFQALDADGAVLADETW 148
                                           *******************99987433337899999988888888**************************** PP

                             TIGR00720 143 ysvGGGfivdeeelkkeeeeee....evpypfksaaellelCkeeglsisevvlenekalrseeevrakllei 211
                                           +svGGGfiv+e e +  ++e +    +vp+pf++a+ell++C+++glsis+v+l++e ++r+eee+ra ll+i
  NCBI__GCF_001482365.1:WP_058857171.1 149 FSVGGGFIVQEGEEDAAAAELDeaskQVPHPFRTARELLAHCRATGLSISDVMLADERTWRTEEEIRAGLLHI 221
                                           *********99877665544333455*********************************************** PP

                             TIGR00720 212 wkvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaP 284
                                           w+vme+c + +l++ g+lpGglkv rra++++++l++++   +dp    +wvnl+alavneena+GgrvvtaP
  NCBI__GCF_001482365.1:WP_058857171.1 222 WDVMEQCKDSSLRRTGTLPGGLKVARRAPAWHDRLRREDPD-RDPSYWQEWVNLVALAVNEENASGGRVVTAP 293
                                           ***********************************998877.8****************************** PP

                             TIGR00720 285 tnGaagiiPavlayykkfve...............easeekvvrflltagaiGilykenasisgaevGCqgev 342
                                           tnGaagiiPavl y++++v+               ++ e +vvrfll+aga+G+lyke+asisgaevGCqgev
  NCBI__GCF_001482365.1:WP_058857171.1 294 TNGAAGIIPAVLFYATHYVPevrramaggdaeelrRVRESVVVRFLLAAGAVGVLYKEQASISGAEVGCQGEV 366
                                           *****************887666677777666565677889******************************** PP

                             TIGR00720 343 GvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgk 415
                                           G+a+smaa+glae+lggtpeqvenaaeiamehnlGltCdP+gGlvq+PCiernaiaa kainaa++al +dg+
  NCBI__GCF_001482365.1:WP_058857171.1 367 GSASSMAAGGLAEVLGGTPEQVENAAEIAMEHNLGLTCDPIGGLVQVPCIERNAIAAAKAINAAKMALWGDGT 439
                                           ************************************************************************* PP

                             TIGR00720 416 kkvsldkvietmretGkdmkakyketskgGlavkv 450
                                           ++vsld+vi tmretGkdm++kyket+ gGlav+v
  NCBI__GCF_001482365.1:WP_058857171.1 440 HRVSLDEVIVTMRETGKDMSHKYKETALGGLAVNV 474
                                           *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (477 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.50
//
[ok]

This GapMind analysis is from Sep 24 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 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