Alignments for a candidate for serA in Caminibacter mediatlanticus TB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Caminibacter mediatlanticus TB-2

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_007472804.1 CMTB2_RS00125 phosphoglycerate dehydrogenase

Query= curated2:Q58424
         (524 letters)



>NCBI__GCF_000170735.1:WP_007472804.1
          Length = 522

 Score =  370 bits (951), Expect = e-107
 Identities = 200/522 (38%), Positives = 326/522 (62%), Gaps = 7/522 (1%)

Query: 2   VKILVTDPLHEDAIKILEEVGEVEV--ATGLTKEELLEKIKDADVLVVRSGTKVTRDVIE 59
           +K ++ DP+H   ++IL++  ++EV  A+   K+ELL+ I+DAD ++ RS T V    + 
Sbjct: 1   MKAVICDPIHPAGVEILKKAKDIEVVDASKTPKDELLKIIEDADGVITRSPTPVDEKFLS 60

Query: 60  KAEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQAT 119
            A+KLK I RAGVGVDN+D+EA +++GI+V+N P A++++  ELTM  +L AAR+   A 
Sbjct: 61  HAKKLKAIVRAGVGVDNVDIEACSKRGIVVMNIPTANTLAAVELTMAHLLTAARSFTNAV 120

Query: 120 ASLKRG-EWDRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAE 178
            +LK+  EW+R+++ GIEL GK LG+IG G IG +V  RAKA  M++I YDPYI    A 
Sbjct: 121 WNLKKEHEWNREKWLGIELAGKKLGIIGFGNIGSRVGIRAKALEMDVIAYDPYIDPSKAT 180

Query: 179 SMGVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEK 238
            +G +   D +E+ K  DFIT+H P TP+T ++I +++I  MK   +++NCARGGL +E 
Sbjct: 181 DLGCKYTTDFDEILK-CDFITIHTPKTPETINMITKKEIEKMKDGVVLINCARGGLYNEN 239

Query: 239 ALYEALKEGKIRAAALDVFEEEPPKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQI 298
            +YE LK GKIR   +DVFE+EP  ++P   L+N   TPH GA+T+E+Q+      AE I
Sbjct: 240 DVYEGLKSGKIRWLGIDVFEKEPVTEHPFFELENTSVTPHIGANTKESQQRIAIQAAEAI 299

Query: 299 KKVLRGELAENVVNMPNIPQEKLGKLKPYMLLAEMLGNIVMQVLDGSVNRVELIYSGELA 358
            + LRG    N +N+P         +  Y+ LA+ +  ++ Q++   + +V++  SG+++
Sbjct: 300 IEALRGSSYPNALNLPINTANTPEWVIKYLELAQKMSYLLSQIIKKPIKKVKVSLSGDIS 359

Query: 359 KEKTDLIKRAFLKGLLSPILLAGINLVNAPIIAKNRNINVVESSTSEEKYGNAIKITAES 418
            E+  ++  + L GLL  I    +N VNA ++A+ + I         E Y N ++I   +
Sbjct: 360 NEEKSVLTFS-LVGLLKNI-TDNVNYVNALVLAEEKGIETEVKKEKNETYKNLVQIKVLT 417

Query: 419 DKKKFSIVGAIINNKPVILEVDGYEVSFIPEGVLAIIKHIDRPGTIGRVCITLGDYGINI 478
           D+ ++SI G ++ N P ++E  G+++ F P+G +   K+ D PG IG V +TL  + INI
Sbjct: 418 DEGEYSISGTMLENHPRVVEFKGFDLEFEPKGKMIFFKNTDVPGVIGEVGMTLAKHNINI 477

Query: 479 ASMQVGRKEPGGESVMLLNLDHTVPEEVIEKIKEIPNIKDVA 520
           A  ++GR +  G+++ ++ +D+ V EEV+ ++K++     VA
Sbjct: 478 ADFRLGRNKE-GQAMAVIIVDNDVNEEVLNELKKLKAALSVA 518


Lambda     K      H
   0.316    0.137    0.372 

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: 705
Number of extensions: 34
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: 524
Length of database: 522
Length adjustment: 35
Effective length of query: 489
Effective length of database: 487
Effective search space:   238143
Effective search space used:   238143
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 52 (24.6 bits)

Align candidate WP_007472804.1 CMTB2_RS00125 (phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

# 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.aa/TIGR01327.hmm
# target sequence database:        /tmp/gapView.1691849.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01327  [M=525]
Accession:   TIGR01327
Description: PGDH: phosphoglycerate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.6e-198  644.9   7.5   6.2e-198  644.7   7.5    1.0  1  NCBI__GCF_000170735.1:WP_007472804.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170735.1:WP_007472804.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.7   7.5  6.2e-198  6.2e-198       2     524 ..       3     521 ..       2     522 .] 0.97

  Alignments for each domain:
  == domain 1  score: 644.7 bits;  conditional E-value: 6.2e-198
                             TIGR01327   2 vlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                            +++d+++++g+e l k k++ev  +++  k+ell++i+d+d++i+RS t+v+e++l++a+kLk i+RaGvGv
  NCBI__GCF_000170735.1:WP_007472804.1   3 AVICDPIHPAGVEiLKKAKDIEVVDASKTPKDELLKIIEDADGVITRSPTPVDEKFLSHAKKLKAIVRAGVGV 75 
                                           58***********6677899***************************************************** PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvke.kkWerkkflGtElygktlGviG 145
                                           DN+diea++k+Gi+v+N+P++nt++a+El++a+ll++aR++++a  ++k+ ++W+r+k+lG+El gk+lG+iG
  NCBI__GCF_000170735.1:WP_007472804.1  76 DNVDIEACSKRGIVVMNIPTANTLAAVELTMAHLLTAARSFTNAVWNLKKeHEWNREKWLGIELAGKKLGIIG 148
                                           *********************************************99975167******************** PP

                             TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218
                                           +G+iGs+v+ rakal+m+v+ayDPyi ++ka++lg+++++d+de+l ++D+it+H+P+t+et+++i k+e++k
  NCBI__GCF_000170735.1:WP_007472804.1 149 FGNIGSRVGIRAKALEMDVIAYDPYIDPSKATDLGCKYTTDFDEIL-KCDFITIHTPKTPETINMITKKEIEK 220
                                           **********************************************.9************************* PP

                             TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvav 291
                                           mK+gv+++NcaRGG+++E+ ++e l++gk+r++++DvfekEP+t+++++el+n +vtpH+gA+t+E+q+++a+
  NCBI__GCF_000170735.1:WP_007472804.1 221 MKDGVVLINCARGGLYNENDVYEGLKSGKIRWLGIDVFEKEPVTEHPFFELENTSVTPHIGANTKESQQRIAI 293
                                           ************************************************************************* PP

                             TIGR01327 292 evaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesell 364
                                           + ae ++eal+g++ ++a+Nlp  +a++ e +  yl+la+k+ +l sq+ k+ +kkv+v+l+G++++ee ++l
  NCBI__GCF_000170735.1:WP_007472804.1 294 QAAEAIIEALRGSSYPNALNLPINTANTPEWVIKYLELAQKMSYLLSQIIKKPIKKVKVSLSGDISNEEKSVL 366
                                           *********************************************************************7777 PP

                             TIGR01327 365 tsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepri 437
                                            ++ l gllk++++ +vn+vnA ++a+e+gi+ e++ke++ e+yknl+++kv +d+ge s++gt+le+ +pr+
  NCBI__GCF_000170735.1:WP_007472804.1 367 -TFSLVGLLKNITD-NVNYVNALVLAEEKGIETEVKKEKN-ETYKNLVQIKVLTDEGEYSISGTMLEN-HPRV 435
                                           .8899*****9887.9****************99987766.99************************6.**** PP

                             TIGR01327 438 veidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevlee 510
                                           ve +gf++++ep+g+++++kn+D+pGvig+vg++l++++iNia+++lgr+++g +a++++ +D++v+eevl+e
  NCBI__GCF_000170735.1:WP_007472804.1 436 VEFKGFDLEFEPKGKMIFFKNTDVPGVIGEVGMTLAKHNINIADFRLGRNKEG-QAMAVIIVDNDVNEEVLNE 507
                                           *************************************************9887.9****************** PP

                             TIGR01327 511 ikevpeiksvklve 524
                                           +k+++++ sv++ e
  NCBI__GCF_000170735.1:WP_007472804.1 508 LKKLKAALSVAYAE 521
                                           *******9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (522 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: 17.64
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis