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_058857687.1 AS188_RS03555 L-serine ammonia-lyase

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



>NCBI__GCF_001482365.1:WP_058857687.1
          Length = 466

 Score =  607 bits (1564), Expect = e-178
 Identities = 310/466 (66%), Positives = 363/466 (77%), Gaps = 8/466 (1%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60
           M+LSV DLF +GIGPSSSHTVGPMRAA RFAEGLR D LL+    V+ ELYGSLGATG G
Sbjct: 1   MALSVLDLFSVGIGPSSSHTVGPMRAARRFAEGLRADGLLDQVARVQSELYGSLGATGWG 60

Query: 61  HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIR-KP 119
           HGSDKAV+LGL GE P+TVDT+T D  ++     G L L G   + F+    + + R K 
Sbjct: 61  HGSDKAVVLGLLGEDPETVDTDTADDTVRTTGERGELLLAGVRPVPFDRSGDVVLHRRKS 120

Query: 120 LAFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKD 179
           L  HPNGM FRA  A G  +R R YYSVGGGFVVDE AAGADR+V DAT +  PF+S  +
Sbjct: 121 LPAHPNGMTFRALGADGQVLRERTYYSVGGGFVVDEQAAGADRVVADATVVPHPFRSGAE 180

Query: 180 LLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGC-RNEGILPGGLK 238
           LL  C   GLSI++VML NE AWRP+ +TR  LL+IW VMQ+CV  GC R E  LPGGLK
Sbjct: 181 LLAICRREGLSIAEVMLANERAWRPDEQTREALLRIWAVMQECVENGCTRPEPTLPGGLK 240

Query: 239 VKRRAAALHRQLCKNPEAA------LRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNG 292
           V+RRA AL  +L +   AA      + DPL  ++WVNL+ALAVNEENA GGR+VTAPTNG
Sbjct: 241 VRRRAPALRARLQELEAAAAAAPGRVDDPLRAMEWVNLFALAVNEENASGGRIVTAPTNG 300

Query: 293 AAGIIPAVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACS 352
           AAGIIPAVLHY+ RF+PGA +DGVVRFLLTA AIGIL KENASISGAEVGCQGEVG ACS
Sbjct: 301 AAGIIPAVLHYWARFVPGADDDGVVRFLLTAGAIGILIKENASISGAEVGCQGEVGSACS 360

Query: 353 MAAGALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVR 412
           MAA  LC VLGG+ +QVENAAE+G+EHNLGLTCDP+GGLVQ+PCIERNA+ SVKA+NA R
Sbjct: 361 MAAAGLCAVLGGTPEQVENAAEVGIEHNLGLTCDPVGGLVQIPCIERNAIASVKAVNAAR 420

Query: 413 MAMRGDGHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           +A++GDG H VSLD+ ++TMR+TG DMK KYKET+RGGLAVN++EC
Sbjct: 421 LALQGDGEHKVSLDQAVKTMRETGKDMKIKYKETSRGGLAVNVVEC 466


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: 782
Number of extensions: 30
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: 466
Length adjustment: 33
Effective length of query: 425
Effective length of database: 433
Effective search space:   184025
Effective search space used:   184025
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_058857687.1 AS188_RS03555 (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.1189369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-212  692.8   0.0   1.2e-212  692.6   0.0    1.0  1  NCBI__GCF_001482365.1:WP_058857687.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001482365.1:WP_058857687.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.6   0.0  1.2e-212  1.2e-212       2     450 .]       4     463 ..       3     463 .. 0.97

  Alignments for each domain:
  == domain 1  score: 692.6 bits;  conditional E-value: 1.2e-212
                             TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelp 74 
                                           sv+dlf++GiGPssshtvGPm+aa++f+e l+  g l+qv+rv+ +lyGsl++tG Gh++dkav+lGl Ge+p
  NCBI__GCF_001482365.1:WP_058857687.1   4 SVLDLFSVGIGPSSSHTVGPMRAARRFAEGLRADGLLDQVARVQSELYGSLGATGWGHGSDKAVVLGLLGEDP 76 
                                           9************************************************************************ PP

                             TIGR00720  75 eevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvG 146
                                           e+vd++++++ +++  e+++l la+   + fd++ d++++ +++lp h+ng++++a+  +g+vl+e+tyysvG
  NCBI__GCF_001482365.1:WP_058857687.1  77 ETVDTDTADDTVRTTGERGELLLAGVRPVPFDRSGDVVLHrRKSLPAHPNGMTFRALGADGQVLRERTYYSVG 149
                                           ****************************************999****************************** PP

                             TIGR00720 147 GGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmee 217
                                           GGf+vde++++ ++  ++   vp+pf+s aell++C++eglsi+ev+l+ne a+r++e++r++ll+iw vm+e
  NCBI__GCF_001482365.1:WP_058857687.1 150 GGFVVDEQAAGADRVVADatVVPHPFRSGAELLAICRREGLSIAEVMLANERAWRPDEQTREALLRIWAVMQE 222
                                           *********9988776655589*************************************************** PP

                             TIGR00720 218 cierglk.aegvlpGglkvkrraaslkrklkakeets.......kdplavldwvnlyalavneenaaGgrvvt 282
                                           c+e+g++  e +lpGglkv+rra++l+++l++ e +         dpl++++wvnl+alavneena+Ggr+vt
  NCBI__GCF_001482365.1:WP_058857687.1 223 CVENGCTrPEPTLPGGLKVRRRAPALRARLQELEAAAaaapgrvDDPLRAMEWVNLFALAVNEENASGGRIVT 295
                                           ******9789********************98776544445556799************************** PP

                             TIGR00720 283 aPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglae 355
                                           aPtnGaagiiPavl+y+ +fv+ a ++ vvrflltagaiGil kenasisgaevGCqgevG+acsmaaagl++
  NCBI__GCF_001482365.1:WP_058857687.1 296 APTNGAAGIIPAVLHYWARFVPGADDDGVVRFLLTAGAIGILIKENASISGAEVGCQGEVGSACSMAAAGLCA 368
                                           ************************************************************************* PP

                             TIGR00720 356 llggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmr 428
                                           +lggtpeqvenaae+++ehnlGltCdPvgGlvqiPCiernaia+vka+naarlal++dg++kvsld+ ++tmr
  NCBI__GCF_001482365.1:WP_058857687.1 369 VLGGTPEQVENAAEVGIEHNLGLTCDPVGGLVQIPCIERNAIASVKAVNAARLALQGDGEHKVSLDQAVKTMR 441
                                           ************************************************************************* PP

                             TIGR00720 429 etGkdmkakyketskgGlavkv 450
                                           etGkdmk kykets+gGlav+v
  NCBI__GCF_001482365.1:WP_058857687.1 442 ETGKDMKIKYKETSRGGLAVNV 463
                                           ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (466 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: 00:00:00.01
# Mc/sec: 15.95
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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