GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Phaeobacter inhibens BS107

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate GFF3560 PGA1_c36140 D-3-phosphoglycerate dehydrogenase SerA

Query= CharProtDB::CH_004924
         (525 letters)



>FitnessBrowser__Phaeo:GFF3560
          Length = 531

 Score =  403 bits (1036), Expect = e-117
 Identities = 210/501 (41%), Positives = 312/501 (62%), Gaps = 5/501 (0%)

Query: 3   RVLVSDKMSNDGLQPLIESDFIEIVQKNVADAEDELHT----FDALLVRSATKVTEDLFN 58
           +VL+SDK+S   +Q   +       Q ++   +D+L      +D L +RSATKVT+ + +
Sbjct: 4   KVLISDKLSEAAVQIFRDRGIDVDFQPDLGKDKDKLAAIIGDYDGLAIRSATKVTQKILD 63

Query: 59  KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118
             T+LK++ RAG+G DNID D A++ GVIV+N P GN I+TAEH  AM+ ++ R IP+A+
Sbjct: 64  NATNLKVIARAGIGTDNIDKDAASQKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEAS 123

Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178
            S  + +W ++ ++G EL  KTLG++G G IG  +  R     M V  +DPFL++E+A K
Sbjct: 124 ASTHAGKWEKSKFMGVELTNKTLGVIGAGNIGGIVCDRARGLKMKVVAYDPFLSQEKADK 183

Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238
           IGV     +E+L  AD IT+H PLT +T+ +L+KE + KTKKGVR+INCARGG++DEAAL
Sbjct: 184 IGVEKVELDELLARADFITLHVPLTDQTRNILSKENLEKTKKGVRIINCARGGLVDEAAL 243

Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298
            E L +GHVAGAA DVF  EP   N L   P V+ TPHLGA+T EAQ NVA QV+E++  
Sbjct: 244 AELLTSGHVAGAAFDVFSEEPAKTNPLFGLPNVVCTPHLGAATSEAQENVALQVAEQMSN 303

Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358
           +     V +A+N+P+MT +E   + P+  ++G +G  + Q   EP+Q + I Y+G  +++
Sbjct: 304 YLLDGAVENALNMPSMTAEEARVMGPWVALSGHLGGFIGQMTDEPIQAINILYDGVASEM 363

Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418
             + +  ++++G +K +++  VN V+A  VA+ERGI  S         +D  I V V   
Sbjct: 364 NLAALNCSVVAGIMK-KLNPDVNMVSAPVVARERGIQISTTNQDKSGTFDGYIKVTVVTS 422

Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478
           +   +V  T       R ++I G NID     H++Y  ++D  G+IG +G+ILGD  +NI
Sbjct: 423 KRERSVAGTVFSDGKPRFIQIKGINIDAEVGAHMLYTTNEDVPGIIGTLGQILGDMGVNI 482

Query: 479 ATMQVGRKEKGGEAIMMLSFD 499
           A   +GR E GGEAI +L  D
Sbjct: 483 ANFTLGRSEAGGEAIALLYVD 503


Lambda     K      H
   0.317    0.134    0.374 

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: 615
Number of extensions: 20
Number of successful extensions: 2
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: 525
Length of database: 531
Length adjustment: 35
Effective length of query: 490
Effective length of database: 496
Effective search space:   243040
Effective search space used:   243040
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate GFF3560 PGA1_c36140 (D-3-phosphoglycerate dehydrogenase SerA)
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.29530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-203  663.2   5.4   1.7e-203  663.0   5.4    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3560  PGA1_c36140 D-3-phosphoglycerate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3560  PGA1_c36140 D-3-phosphoglycerate dehydrogenase SerA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  663.0   5.4  1.7e-203  1.7e-203       1     521 [.       4     524 ..       4     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 663.0 bits;  conditional E-value: 1.7e-203
                          TIGR01327   1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvigRaGvGvD 74 
                                        kvl++dklse++++++++++++vd + +l  +k++l ++i dyd+l +RSatkvt+++l++a++Lkvi+RaG+G D
  lcl|FitnessBrowser__Phaeo:GFF3560   4 KVLISDKLSEAAVQIFRDRGIDVDFQPDLgkDKDKLAAIIGDYDGLAIRSATKVTQKILDNATNLKVIARAGIGTD 79 
                                        7*************************998335678999************************************** PP

                          TIGR01327  75 NidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGlGriG 150
                                        Nid +aa++kG++v+N+P gn i++aE+a+a+++a+aR+ip+a +s++++kWe++kf+G+El++ktlGviG+G+iG
  lcl|FitnessBrowser__Phaeo:GFF3560  80 NIDKDAASQKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEASASTHAGKWEKSKFMGVELTNKTLGVIGAGNIG 155
                                        **************************************************************************** PP

                          TIGR01327 151 sevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakmKkgviiv 226
                                         +v +ra++l+mkv+ayDP++s+eka+k+gve+++ ldella+aD+it+HvPlt++t+++++ke+l+k+Kkgv+i+
  lcl|FitnessBrowser__Phaeo:GFF3560 156 GIVCDRARGLKMKVVAYDPFLSQEKADKIGVEKVE-LDELLARADFITLHVPLTDQTRNILSKENLEKTKKGVRII 230
                                        ********************************666.**************************************** PP

                          TIGR01327 227 NcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvavevaeevlealk 302
                                        NcaRGG++dE+AL+e+l++g+v++aa+Dvf++EP++ n+l+ l+nvv tpHlgA t+Eaqenva++vae+++++l 
  lcl|FitnessBrowser__Phaeo:GFF3560 231 NCARGGLVDEAALAELLTSGHVAGAAFDVFSEEPAKTNPLFGLPNVVCTPHLGAATSEAQENVALQVAEQMSNYLL 306
                                        **************************************************************************** PP

                          TIGR01327 303 gevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeeselltsallkgllkevle 378
                                        + +ve+a+N+p+++aee+  + p+++l+ +lG +++q+++e ++++++ + G  +e++  +l+ ++++g++k+ l+
  lcl|FitnessBrowser__Phaeo:GFF3560 307 DGAVENALNMPSMTAEEARVMGPWVALSGHLGGFIGQMTDEPIQAINILYDGVASEMNLAALNCSVVAGIMKK-LN 381
                                        **********************************************************************986.78 PP

                          TIGR01327 379 eevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriveidgfevdlepegill 454
                                         +vn+v+A++va+ergi+++ +++++s +++ +++v+v ++k e+svagtv+++ +pr ++i+g+++d e   ++l
  lcl|FitnessBrowser__Phaeo:GFF3560 382 PDVNMVSAPVVARERGIQISTTNQDKSGTFDGYIKVTVVTSKRERSVAGTVFSDGKPRFIQIKGINIDAEVGAHML 457
                                        8*************************************************************************** PP

                          TIGR01327 455 iiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleeikevpeiksvk 521
                                        +++n+D+pG+ig +g++lg++g+Nia+++lgr+e+ggea++ll +De+v++   ++++e +  +++k
  lcl|FitnessBrowser__Phaeo:GFF3560 458 YTTNEDVPGIIGTLGQILGDMGVNIANFTLGRSEAGGEAIALLYVDEPVPAAARAALAETEFFNQIK 524
                                        ****************************************************999999988777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (531 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.27
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

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:

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:

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:

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