Alignments for a candidate for rocD in Flavobacterium sp. LM5

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.2218723.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.87
//
[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:

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