Alignments for a candidate for sdaB in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Marivita geojedonensis DPG-138

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_085636343.1 MGEO_RS08740 L-serine ammonia-lyase

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



>NCBI__GCF_002115805.1:WP_085636343.1
          Length = 457

 Score =  466 bits (1200), Expect = e-136
 Identities = 242/459 (52%), Positives = 312/459 (67%), Gaps = 3/459 (0%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKG 60
           M LSVFD+FK+GIGPSSSHT+GPM AAARF + LR+         VK  L+GSL  TG G
Sbjct: 1   MFLSVFDMFKVGIGPSSSHTMGPMVAAARFLDRLRKAPFT--VAGVKASLHGSLAFTGVG 58

Query: 61  HGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIRKP- 119
           H +D+A +LGL G  P++ D E  DA L  I+++  +       + F+ +  L     P 
Sbjct: 59  HATDRATILGLAGFVPESYDREKADAALAQIKATRTVEPESLPVLAFDPESDLTFDFGPN 118

Query: 120 LAFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAKD 179
           L  H NGMI  A DA G  +    YYS+GGGFV+ +    A +  +D  P+ +PFKSA +
Sbjct: 119 LPGHANGMILSATDAQGDVILQETYYSIGGGFVMTQAELDAGKDTDDGAPVPYPFKSAAE 178

Query: 180 LLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLKV 239
           +L   +   +SI+++   NE + R  AE   G+ ++WQVM DC+  G   EGILPGGL V
Sbjct: 179 MLEMANIAHMSIAEMKRANELSRRSAAELDRGIERLWQVMNDCINRGLEAEGILPGGLSV 238

Query: 240 KRRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIPA 299
           KRRA  +H++L       L  P ++ DW+++YA+AVNEENA GG+VVTAPTNGAAG++PA
Sbjct: 239 KRRAKGIHQKLLAERGMNLTAPHTINDWMSVYAMAVNEENAAGGQVVTAPTNGAAGVVPA 298

Query: 300 VLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGALC 359
            + YY+  +PGA+   V  FLLTAAAIG L K NASISGAE GCQ EVG A +MAA  LC
Sbjct: 299 TIRYYLDHVPGATTKRVPDFLLTAAAIGGLVKFNASISGAEAGCQAEVGSASAMAAAGLC 358

Query: 360 EVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGDG 419
            V+GGS +Q+ENAAEI +EH+LG+TCDP+ GLVQVPCIERN +G++KA++A  +A+RGDG
Sbjct: 359 AVMGGSPEQIENAAEIALEHHLGMTCDPVKGLVQVPCIERNGLGAIKAVSAASLALRGDG 418

Query: 420 HHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
            HFV LD  I TMRQTGADM  KYKET+ GGLAVNI  C
Sbjct: 419 THFVPLDSAIETMRQTGADMHEKYKETSLGGLAVNIPNC 457


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: 594
Number of extensions: 24
Number of successful extensions: 3
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: 457
Length adjustment: 33
Effective length of query: 425
Effective length of database: 424
Effective search space:   180200
Effective search space used:   180200
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_085636343.1 MGEO_RS08740 (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.1177841.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-186  606.6   0.4   1.8e-186  606.4   0.4    1.0  1  NCBI__GCF_002115805.1:WP_085636343.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085636343.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  606.4   0.4  1.8e-186  1.8e-186       2     450 .]       4     454 ..       3     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 606.4 bits;  conditional E-value: 1.8e-186
                             TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelp 74 
                                           svfd+fk+GiGPsssht+GPm aa++f+++l+k+    +v+ vk  l+Gsla+tG Gh+td+a +lGl+G+ p
  NCBI__GCF_002115805.1:WP_085636343.1   4 SVFDMFKVGIGPSSSHTMGPMVAAARFLDRLRKA--PFTVAGVKASLHGSLAFTGVGHATDRATILGLAGFVP 74 
                                           9******************************887..56899******************************** PP

                             TIGR00720  75 eevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvG 146
                                           e+ d e++++ l++++++++++ ++   + fd e+dl+f+   +lp h+ng+ l+a d +g+v+ ++tyys+G
  NCBI__GCF_002115805.1:WP_085636343.1  75 ESYDREKADAALAQIKATRTVEPESLPVLAFDPESDLTFDfGPNLPGHANGMILSATDAQGDVILQETYYSIG 147
                                           ****************************************999****************************** PP

                             TIGR00720 147 GGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmee 217
                                           GGf+++++el+  +++++   vpypfksaae+le+ +  ++si+e+  +ne + rs +e ++ + ++w+vm++
  NCBI__GCF_002115805.1:WP_085636343.1 148 GGFVMTQAELDAGKDTDDgaPVPYPFKSAAEMLEMANIAHMSIAEMKRANELSRRSAAELDRGIERLWQVMND 220
                                           *******99987777766669**************************************************** PP

                             TIGR00720 218 cierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaa 289
                                           ci+rgl+aeg+lpGgl vkrra+ +++kl a++ ++ ++p ++ dw+++ya+avneenaaGg+vvtaPtnGaa
  NCBI__GCF_002115805.1:WP_085636343.1 221 CINRGLEAEGILPGGLSVKRRAKGIHQKLLAERGMNlTAPHTINDWMSVYAMAVNEENAAGGQVVTAPTNGAA 293
                                           *********************************99988999999***************************** PP

                             TIGR00720 290 giiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpe 362
                                           g++Pa ++yy   v+ a+ ++v +fllta+aiG l k nasisgae+GCq+evG+a++maaagl++++gg+pe
  NCBI__GCF_002115805.1:WP_085636343.1 294 GVVPATIRYYLDHVPGATTKRVPDFLLTAAAIGGLVKFNASISGAEAGCQAEVGSASAMAAAGLCAVMGGSPE 366
                                           ************************************************************************* PP

                             TIGR00720 363 qvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmk 435
                                           q+enaaeia+eh+lG+tCdPv Glvq+PCiern+++a+ka++aa lal++dg+++v ld+ ietmr+tG+dm+
  NCBI__GCF_002115805.1:WP_085636343.1 367 QIENAAEIALEHHLGMTCDPVKGLVQVPCIERNGLGAIKAVSAASLALRGDGTHFVPLDSAIETMRQTGADMH 439
                                           ************************************************************************* PP

                             TIGR00720 436 akyketskgGlavkv 450
                                           +kykets gGlav++
  NCBI__GCF_002115805.1:WP_085636343.1 440 EKYKETSLGGLAVNI 454
                                           *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (457 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: 23.87
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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