Alignments for a candidate for sdaB in Nocardiopsis baichengensis YIM 90130

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Nocardiopsis baichengensis YIM 90130

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_017539971.1 C892_RS0108030 L-serine ammonia-lyase

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



>NCBI__GCF_000341205.1:WP_017539971.1
          Length = 470

 Score =  570 bits (1469), Expect = e-167
 Identities = 305/477 (63%), Positives = 347/477 (72%), Gaps = 26/477 (5%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60
           M++SVFDLFKIGIGPSSSHTVGPM+AAA F +GL          S++ +LYGSL  TGKG
Sbjct: 1   MAISVFDLFKIGIGPSSSHTVGPMKAAATFVDGLTASGAAERAASLRCDLYGSLALTGKG 60

Query: 61  HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGE---------HSIEFNEKL 111
           HGSD AV+LGL G+ P+ VD + V   L A+  SGRL L G          H +EF  K 
Sbjct: 61  HGSDTAVILGLLGQTPEGVDPDAVPDLLAAVGESGRLRLGGTGPRVAFDPAHDVEFRRK- 119

Query: 112 HLAMIRKPLAFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLT 171
                 + L  HPNGM F A+DA G ++RSR YYSVGGGFVVDE A G+DRI+ D TP+ 
Sbjct: 120 ------ETLPGHPNGMRFTAYDADGAELRSRVYYSVGGGFVVDEDATGSDRIIPDTTPVP 173

Query: 172 FPFKSAKDLLGHCSTYGLSISQVMLTNESAW-RPEAETRAGLLKIWQVMQDCVAAGCRNE 230
            PF +A++LL  C   G+SIS VML NE A+ R   + R  LL+IW+VM+ CV  G   E
Sbjct: 174 HPFTTAQELLEVCRETGMSISAVMLANERAFGRSPEQVRTELLEIWRVMRACVRRGVTTE 233

Query: 231 GILPGGLKVKRRAAALHRQLCKNPEAA---------LRDPLSVLDWVNLYALAVNEENAY 281
           G LPGGL+V RRA  L+RQL    +A+         L DPL   DW+ LYALAVNEENA 
Sbjct: 234 GTLPGGLRVPRRAHRLYRQLGGRCDASGLVAPDSPDLSDPLHGSDWITLYALAVNEENAA 293

Query: 282 GGRVVTAPTNGAAGIIPAVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEV 341
           GGRVVTAPTNGAAGI+PAVLHYY  F  GASE+GVVRFLLTA AIGIL+KENASISGAEV
Sbjct: 294 GGRVVTAPTNGAAGIVPAVLHYYTHFCRGASEEGVVRFLLTAGAIGILFKENASISGAEV 353

Query: 342 GCQGEVGVACSMAAGALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNA 401
           GCQGEVG A SMAAG L E LG +  QVENAAEI MEHNLGLTCDPIGGLVQVPCIERNA
Sbjct: 354 GCQGEVGSASSMAAGGLAEALGATPSQVENAAEIAMEHNLGLTCDPIGGLVQVPCIERNA 413

Query: 402 MGSVKAINAVRMAMRGDGHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           + SVKA+ A RMAMRGDG HFVSLDKVIRTMR TG DM  KYKET+RGGLAVN+IEC
Sbjct: 414 VASVKAVTATRMAMRGDGSHFVSLDKVIRTMRDTGRDMMDKYKETSRGGLAVNVIEC 470


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: 773
Number of extensions: 34
Number of successful extensions: 4
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: 470
Length adjustment: 33
Effective length of query: 425
Effective length of database: 437
Effective search space:   185725
Effective search space used:   185725
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_017539971.1 C892_RS0108030 (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.148298.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-209  682.7   0.0   1.5e-209  682.5   0.0    1.0  1  NCBI__GCF_000341205.1:WP_017539971.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341205.1:WP_017539971.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  682.5   0.0  1.5e-209  1.5e-209       1     450 []       3     467 ..       3     467 .. 0.95

  Alignments for each domain:
  == domain 1  score: 682.5 bits;  conditional E-value: 1.5e-209
                             TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGel 73 
                                           isvfdlfkiGiGPssshtvGPmkaa++fv+ l+  g  e+ ++++ dlyGslaltGkGh++d+av+lGl G++
  NCBI__GCF_000341205.1:WP_017539971.1   3 ISVFDLFKIGIGPSSSHTVGPMKAAATFVDGLTASGAAERAASLRCDLYGSLALTGKGHGSDTAVILGLLGQT 75 
                                           79*********************************************************************** PP

                             TIGR00720  74 peevdiesieklleeveeekklkla.nqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyys 144
                                           pe vd + +++ll++v e+++l+l+    ++ fd ++d++f+ +e+lp h+ng+r++ayd +g+ l++++yys
  NCBI__GCF_000341205.1:WP_017539971.1  76 PEGVDPDAVPDLLAAVGESGRLRLGgTGPRVAFDPAHDVEFRrKETLPGHPNGMRFTAYDADGAELRSRVYYS 148
                                           ************************966789************899**************************** PP

                             TIGR00720 145 vGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekal.rseeevraklleiwkv 214
                                           vGGGf+vde+++++++   +   vp+pf++a+elle C+e+g+sis+v+l+ne a+ rs e+vr++lleiw+v
  NCBI__GCF_000341205.1:WP_017539971.1 149 VGGGFVVDEDATGSDRIIPDttPVPHPFTTAQELLEVCRETGMSISAVMLANERAFgRSPEQVRTELLEIWRV 221
                                           **********9998886554449*******************************98467899*********** PP

                             TIGR00720 215 meecierglkaegvlpGglkvkrraaslkrklkakeets..........kdplavldwvnlyalavneenaaG 277
                                           m++c++rg+++eg+lpGgl+v+rra++l+r+l  + ++s          +dpl+  dw++lyalavneenaaG
  NCBI__GCF_000341205.1:WP_017539971.1 222 MRACVRRGVTTEGTLPGGLRVPRRAHRLYRQLGGRCDASglvapdspdlSDPLHGSDWITLYALAVNEENAAG 294
                                           *******************************975543322222333346899********************* PP

                             TIGR00720 278 grvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaa 350
                                           grvvtaPtnGaagi+Pavl+yy++f++ asee vvrflltagaiGil+kenasisgaevGCqgevG+a+smaa
  NCBI__GCF_000341205.1:WP_017539971.1 295 GRVVTAPTNGAAGIVPAVLHYYTHFCRGASEEGVVRFLLTAGAIGILFKENASISGAEVGCQGEVGSASSMAA 367
                                           ************************************************************************* PP

                             TIGR00720 351 aglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkv 423
                                           +glae+lg+tp+qvenaaeiamehnlGltCdP+gGlvq+PCierna+a+vka+ a+r+a+++dg+++vsldkv
  NCBI__GCF_000341205.1:WP_017539971.1 368 GGLAEALGATPSQVENAAEIAMEHNLGLTCDPIGGLVQVPCIERNAVASVKAVTATRMAMRGDGSHFVSLDKV 440
                                           ************************************************************************* PP

                             TIGR00720 424 ietmretGkdmkakyketskgGlavkv 450
                                           i+tmr+tG+dm  kykets+gGlav+v
  NCBI__GCF_000341205.1:WP_017539971.1 441 IRTMRDTGRDMMDKYKETSRGGLAVNV 467
                                           *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (470 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: 19.44
//
[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