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

GapMind for catabolism of small carbon sources

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

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate WP_085640330.1 MGEO_RS16410 kynureninase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4288
         (416 letters)



>NCBI__GCF_002115805.1:WP_085640330.1
          Length = 397

 Score =  401 bits (1030), Expect = e-116
 Identities = 204/397 (51%), Positives = 270/397 (68%), Gaps = 7/397 (1%)

Query: 20  RQQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGLIRSWNSAGWRDLPERLGNR 79
           R  F LPEG+IYLDGNSLG  P +A AR    +A EWG+ LI  WN+ GW D+P RLG++
Sbjct: 8   RAAFHLPEGMIYLDGNSLGPLPKSAAARVAQTVASEWGDHLITGWNACGWMDMPARLGDQ 67

Query: 80  LGGLIGAGDGEVVVTDTTSINLFKVLSAALRVQATRAPTRRVIVTETGNFPTDLYIAEGL 139
           +G LIGA  G VVV DT SI +F+ L+AAL++     P RRVI+++TGNFP+DLY+AEGL
Sbjct: 68  IGRLIGAEAGHVVVGDTLSIKVFQALAAALKLN----PHRRVILSDTGNFPSDLYMAEGL 123

Query: 140 ADMLQQGYTLRLVDSPQELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTTLTHECGALAI 199
             +L   Y LRLV +P+E+  AI  + AV ++T V+Y+TG  HDM ALT   H  G + +
Sbjct: 124 ISLLGPDYELRLV-APEEVGAAITDEIAVTLITEVDYRTGRKHDMAALTAKAHANGVVTV 182

Query: 200 WDLAHSAGAVPVDLHQARADYAIGCTYKYLNGGPGSQAFVWVSPELCDLVAQPLSGWFGH 259
           WDLAHSAGA+PVDL  A+AD+AIGCTYKYLNGGPG+ AF++V+P   D+    LSGW GH
Sbjct: 183 WDLAHSAGAIPVDLAGAKADFAIGCTYKYLNGGPGAPAFIYVAPRHADMALPALSGWLGH 242

Query: 260 SRQFAMESHYQPSSGIARYLCGTQPITSLAMVECGLDVFAQTDMASLRSKSLALTDLFIQ 319
              FA +  Y+   GI+R   GT P+  +A ++  LDV+   D+  LR++S+ L++ FI 
Sbjct: 243 DSPFAFDLGYKAGVGISRMRVGTPPVLQMAALDAALDVWDDVDLNDLRTRSIDLSERFIA 302

Query: 320 LVEQRCAAHELTLVTPREHAKRGSHVSFEHPQGYAVIQALIARGVIGDYREPRIMRFGFT 379
            VE  C   +LTL +PR  A+RGS VSF+  +GYA +QALIA  VIGD+R P IMRFGFT
Sbjct: 303 GVEATCP--DLTLASPRNAAERGSQVSFKFEEGYAAMQALIAHKVIGDFRAPDIMRFGFT 360

Query: 380 PLYTSFTEVWDAVQILGDILDQKTWSQEQFQIRHSVT 416
           PLY    +V  AV+ L  I+  + W   +F+ R +VT
Sbjct: 361 PLYLILEDVDQAVERLARIMRDRLWDTPEFKQRKAVT 397


Lambda     K      H
   0.321    0.135    0.412 

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: 463
Number of extensions: 18
Number of successful extensions: 4
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: 416
Length of database: 397
Length adjustment: 31
Effective length of query: 385
Effective length of database: 366
Effective search space:   140910
Effective search space used:   140910
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_085640330.1 MGEO_RS16410 (kynureninase)
to HMM TIGR01814 (kynU: kynureninase (EC 3.7.1.3))

# 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/TIGR01814.hmm
# target sequence database:        /tmp/gapView.3036727.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01814  [M=400]
Accession:   TIGR01814
Description: kynureninase: kynureninase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.1e-93  299.3   0.0    2.7e-93  298.9   0.0    1.1  1  NCBI__GCF_002115805.1:WP_085640330.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085640330.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.9   0.0   2.7e-93   2.7e-93      12     399 ..       6     380 ..       2     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 298.9 bits;  conditional E-value: 2.7e-93
                             TIGR01814  12 alRdeFalpkakdeneviyld.NSLalmpkaak.ealkeeldkWakllveshevgkapWleldealeklla.. 80 
                                           a R +F+lp     + +iyld NSL+  pk+a+ ++ + ++ +W++ l+++++     W++++ +l +     
  NCBI__GCF_002115805.1:WP_085640330.1   6 ATRAAFHLP-----EGMIYLDgNSLGPLPKSAAaRVAQTVASEWGDHLITGWN--ACGWMDMPARLGDQIGrl 71 
                                           6799*****.....88999966****9999865167788899***********..999********8876667 PP

                             TIGR01814  81 lvakekevvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaiesqlklkleveeslvqvepreeet 153
                                           ++a++  vvv ++l++ +++ la+++k  ++R++Il++  +FPsDly++e  + l   ++  l          
  NCBI__GCF_002115805.1:WP_085640330.1  72 IGAEAGHVVVGDTLSIKVFQALAAALKLNPHRRVILSDTGNFPSDLYMAEGLISLL-GPDYEL---------- 133
                                           99*************************************************99998.555555.......... PP

                             TIGR01814 154 lrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava.vpleLhdwdvDfAv 224
                                            rl + ++v ++ +deiA++l+++v Y+t +  d+aa+t++a+++g + v+DLaH+++ +p++L  +++DfA+
  NCBI__GCF_002115805.1:WP_085640330.1 134 -RLVAPEEVGAAITDEIAVTLITEVDYRTgRKHDMAALTAKAHANGVVTVWDLAHSAGaIPVDLAGAKADFAI 205
                                           .5555555888999*******************************************99************** PP

                             TIGR01814 225 wCsYKylnasp.a.agafvhekkakeelprlalwwwhekskrfkmeeklelrpaafrlsnppvlsvaalka.L 294
                                            C+YKyln +p a a ++v +++a   lp+l++w +h+ +++f+  +k+ +  + +r+ +ppvl++aal a L
  NCBI__GCF_002115805.1:WP_085640330.1 206 GCTYKYLNGGPgApAFIYVAPRHADMALPALSGWLGHDSPFAFDLGYKAGVGISRMRVGTPPVLQMAALDAaL 278
                                           ***********55566667788899999***********************99******************** PP

                             TIGR01814 295 elfdqaslealRkkSllLTdyleeLvkarlayklvleiitPedtaer.sqlslkfskedkavlkalkkrdvvi 366
                                           +++d+++l++lR +S+ L + ++  v+a +     l++++P++ aer sq+s+kf+ e +a ++al++++v+ 
  NCBI__GCF_002115805.1:WP_085640330.1 279 DVWDDVDLNDLRTRSIDLSERFIAGVEATCPD---LTLASPRNAAERgSQVSFKFE-EGYAAMQALIAHKVIG 347
                                           *******************************8...*********************.**************** PP

                             TIGR01814 367 DkRePnviRlaPvpLYntfkDvykavevleeil 399
                                           D+R+P+++R+  +pLY   +Dv +ave l  i+
  NCBI__GCF_002115805.1:WP_085640330.1 348 DFRAPDIMRFGFTPLYLILEDVDQAVERLARIM 380
                                           *****************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (397 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.81
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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