GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Flavobacterium sp. LM5

Align Ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_078212259.1 BXU11_RS08775 ornithine--oxo-acid transaminase

Query= reanno::Cola:Echvi_0577
         (413 letters)



>NCBI__GCF_002017945.1:WP_078212259.1
          Length = 427

 Score =  578 bits (1491), Expect = e-170
 Identities = 279/417 (66%), Positives = 337/417 (80%), Gaps = 11/417 (2%)

Query: 6   TSSQQAIELENKHGAHNYHPLPVVLSRGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRI 65
           + S+  IE EN+ GAHNYHPLPVVL RGEGV++WDV+G+KY+DFLS+YSAVNQGHCHP+I
Sbjct: 10  SKSEVLIEKENQFGAHNYHPLPVVLERGEGVYVWDVDGKKYFDFLSAYSAVNQGHCHPKI 69

Query: 66  LQTLIDQAGTLTLTSRAFHNDVLGPFEKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWG 125
           +  +I+QA  LTLTSRAFHND LG FE+++T+YFG+DKVLPMNTGAE VETA+K+ RKW 
Sbjct: 70  IGAMIEQAQKLTLTSRAFHNDKLGVFEEYITDYFGFDKVLPMNTGAEAVETALKLCRKWA 129

Query: 126 YEKKGIPENEGTIIVAKNNFHGRTTTVISFSNDETARKNFGPYTPGFVTIPHDDIDALKD 185
           YE KGIPEN+  +IV +NNFHGRTTT+ISFSNDE ARK+FGP+T GF+ IP+DDIDAL+ 
Sbjct: 130 YEVKGIPENQAQVIVCENNFHGRTTTIISFSNDEGARKSFGPFTEGFIRIPYDDIDALEK 189

Query: 186 VLSQSKNIIGYLVEPIQGEAGVYVPKEGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLL 245
            L  S NI G+LVEPIQGEAGVYVP EGYL +  A+C+ H  LF+ADE+QTGIARTG+LL
Sbjct: 190 ALQSSPNIAGFLVEPIQGEAGVYVPSEGYLAKAKALCEAHNALFIADEVQTGIARTGRLL 249

Query: 246 A----CDHE-------GVKPDMLILGKAISGGFYPVSAVLADDHIMEVIQPGQHGSTFGG 294
           A    C  E        VKPD+LILGKAISGG YPVSAVLA++ IM VI+PGQHGSTFGG
Sbjct: 250 ATCGNCSCEKGCEKTPEVKPDILILGKAISGGVYPVSAVLANNEIMNVIKPGQHGSTFGG 309

Query: 295 NPLGAKVAMTALNVVKDEKLAENADKLGKLFRERIQQLVDKSDLVELVRGKGLLNAIVIN 354
           NP+ A VA+ AL V+KDE LA NAD+LG + R+ +  +  K+ L+ LVRGKGLLNAIVIN
Sbjct: 310 NPVAAAVAIAALEVIKDENLAANADRLGNILRQGLNDIAAKNPLITLVRGKGLLNAIVIN 369

Query: 355 DTEDSDTAWRLCLALKENGLLAKPTHGNIIRFAPPLVITEEQLHDCCDIIEKTIQNF 411
             EDSD AW +CL  ++ GLLAKPTHGN IRFAPPLVI+EEQ+ +C  IIEK + +F
Sbjct: 370 SDEDSDLAWDICLRFRDYGLLAKPTHGNKIRFAPPLVISEEQIQECLAIIEKALNDF 426


Lambda     K      H
   0.318    0.137    0.407 

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: 608
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: 413
Length of database: 427
Length adjustment: 32
Effective length of query: 381
Effective length of database: 395
Effective search space:   150495
Effective search space used:   150495
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_078212259.1 BXU11_RS08775 (ornithine--oxo-acid transaminase)
to HMM TIGR01885 (rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13))

# 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/TIGR01885.hmm
# target sequence database:        /tmp/gapView.1469960.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01885  [M=402]
Accession:   TIGR01885
Description: Orn_aminotrans: ornithine--oxo-acid transaminase
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-197  642.1   0.0   1.8e-197  641.8   0.0    1.0  1  NCBI__GCF_002017945.1:WP_078212259.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002017945.1:WP_078212259.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.8   0.0  1.8e-197  1.8e-197       2     401 ..      13     423 ..      12     424 .. 0.96

  Alignments for each domain:
  == domain 1  score: 641.8 bits;  conditional E-value: 1.8e-197
                             TIGR01885   2 eevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssr 74 
                                           e +ie+e+++gahnyhplpvvl+++eG++vwdv+gk+y+dflsaysavnqGhchpki+ a++eqaqkltl+sr
  NCBI__GCF_002017945.1:WP_078212259.1  13 EVLIEKENQFGAHNYHPLPVVLERGEGVYVWDVDGKKYFDFLSAYSAVNQGHCHPKIIGAMIEQAQKLTLTSR 85 
                                           6689********************************************************************* PP

                             TIGR01885  75 afyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavis 147
                                           af+nd++g f+ey+t++fG+dkvlpmntGaeaveta+kl+rkW+y++k+ipe++a+++++e+nfhGrt ++is
  NCBI__GCF_002017945.1:WP_078212259.1  86 AFHNDKLGVFEEYITDYFGFDKVLPMNTGAEAVETALKLCRKWAYEVKGIPENQAQVIVCENNFHGRTTTIIS 158
                                           ************************************************************************* PP

                             TIGR01885 148 lstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckkyn 220
                                            s+d+ +r+ fGp+++++ +i+y++++ale+al++ ++++a+flvePiqGeaGv vp++gyl k+++lc+ +n
  NCBI__GCF_002017945.1:WP_078212259.1 159 FSNDEGARKSFGPFTEGFIRIPYDDIDALEKALQS-SPNIAGFLVEPIQGEAGVYVPSEGYLAKAKALCEAHN 230
                                           **********************************9.9************************************ PP

                             TIGR01885 221 vlliadeiqtGiartGkll.......avehe.......evkPdivllGkalsgGvyPvsavladkevmltikp 279
                                            l+iade+qtGiartG+ll       +   e       evkPdi++lGka+sgGvyPvsavla++e+m +ikp
  NCBI__GCF_002017945.1:WP_078212259.1 231 ALFIADEVQTGIARTGRLLatcgncsC---EkgcektpEVKPDILILGKAISGGVYPVSAVLANNEIMNVIKP 300
                                           *******************44333220...133334459********************************** PP

                             TIGR01885 280 gehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkkl..kkeivkevrGkGllnaivideska 350
                                           g+hGst+gGnP+a+ava+aalev+k+e+la +a++lG++lr+ l+++  k+++++ vrGkGllnaivi++++ 
  NCBI__GCF_002017945.1:WP_078212259.1 301 GQHGSTFGGNPVAAAVAIAALEVIKDENLAANADRLGNILRQGLNDIaaKNPLITLVRGKGLLNAIVINSDE- 372
                                           **********************************************98788*******************99. PP

                             TIGR01885 351 ngreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401
                                           ++  awd+cl++++ Gllakpth++ ir+aPPlvi+ee+++e++ ii+k+l
  NCBI__GCF_002017945.1:WP_078212259.1 373 DSDLAWDICLRFRDYGLLAKPTHGNKIRFAPPLVISEEQIQECLAIIEKAL 423
                                           999*********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (427 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: 00:00:00.00
# Mc/sec: 24.94
//
[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:

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