Alignments for a candidate for L-LDH in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for L-LDH in Azospirillum brasilense Sp245

Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate AZOBR_RS01310 AZOBR_RS01310 lactate dehydrogenase

Query= SwissProt::Q5SJA1
         (310 letters)



>FitnessBrowser__azobra:AZOBR_RS01310
          Length = 313

 Score =  377 bits (967), Expect = e-109
 Identities = 199/304 (65%), Positives = 234/304 (76%)

Query: 1   MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAG 60
           MKVGIVG+G VG+   +A+ + G A EVVLVD++ KLA A A+DI HA PFA    VR G
Sbjct: 1   MKVGIVGAGAVGATAGFAMVMSGAASEVVLVDMNEKLAAAQAQDIAHAVPFARAAQVRHG 60

Query: 61  SYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVD 120
            Y  L GA  VVLAAGVAQRPGETRLQLL+RNA VF  ++P VL AAP+A+LLVATNP+D
Sbjct: 61  GYAALAGAGVVVLAAGVAQRPGETRLQLLERNAAVFGAIIPAVLAAAPDAILLVATNPLD 120

Query: 121 VMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVW 180
           VMTQ+A R+SGLPP RV+GSGTILDTARFRALLA+ L V P+SVHA+V+GEHGDSEVL+W
Sbjct: 121 VMTQIATRISGLPPSRVIGSGTILDTARFRALLADRLGVTPKSVHAHVVGEHGDSEVLLW 180

Query: 181 SSAQVGGVPLLEFAEARGRALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVR 240
           S A V  +P+   AE   R L+ EDRA IDEGVRRAAY II+GKG T +GIG GL+R+V 
Sbjct: 181 SGATVACLPVDRGAERLKRPLTAEDRAAIDEGVRRAAYHIIDGKGHTAFGIGGGLSRIVA 240

Query: 241 AILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEI 300
           AI  DE+ V T S    EV GV +V+LSLPR++GAGGV  TV P LS EE  AL+RSAEI
Sbjct: 241 AIAGDERAVLTCSILNDEVLGVPDVALSLPRVIGAGGVLETVMPDLSEEEAAALKRSAEI 300

Query: 301 LKEA 304
           LKEA
Sbjct: 301 LKEA 304


Lambda     K      H
   0.319    0.136    0.384 

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: 336
Number of extensions: 7
Number of successful extensions: 1
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: 310
Length of database: 313
Length adjustment: 27
Effective length of query: 283
Effective length of database: 286
Effective search space:    80938
Effective search space used:    80938
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate AZOBR_RS01310 AZOBR_RS01310 (lactate dehydrogenase)
to HMM TIGR01771 (L-lactate dehydrogenase (EC 1.1.1.27))

# 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/TIGR01771.hmm
# target sequence database:        /tmp/gapView.16248.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01771  [M=299]
Accession:   TIGR01771
Description: L-LDH-NAD: L-lactate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-106  341.6   0.0   2.3e-106  341.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS01310  AZOBR_RS01310 lactate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS01310  AZOBR_RS01310 lactate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.5   0.0  2.3e-106  2.3e-106       1     299 []       5     303 ..       5     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 341.5 bits;  conditional E-value: 2.3e-106
                                 TIGR01771   1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvv 69 
                                               i+GagaVG+++ fa++++g a+e+vl+D+ne+ a ++a d+++a++f+ + ++v++g y+ l++a +vv
  lcl|FitnessBrowser__azobra:AZOBR_RS01310   5 IVGAGAVGATAGFAMVMSGAASEVVLVDMNEKLAAAQAQDIAHAVPFA-RAAQVRHGGYAALAGAGVVV 72 
                                               8***********************************************.679***************** PP

                                 TIGR01771  70 itaGaeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsG 138
                                               ++aG +q+pgetRl+l+e+n++++  i++ v ++++d+illv++NP+D++t++++++sglp++rviGsG
  lcl|FitnessBrowser__azobra:AZOBR_RS01310  73 LAAGVAQRPGETRLQLLERNAAVFGAIIPAVLAAAPDAILLVATNPLDVMTQIATRISGLPPSRVIGSG 141
                                               ********************************************************************* PP

                                 TIGR01771 139 tvLdtaRlrrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelk.eie 206
                                               t+LdtaR+r+lla++l+v pksvha+v+GEHGdsev +ws a++a +p+++ +e  ++   +e++ +i+
  lcl|FitnessBrowser__azobra:AZOBR_RS01310 142 TILDTARFRALLADRLGVTPKSVHAHVVGEHGDSEVLLWSGATVACLPVDRGAERLKRPLTAEDRaAID 210
                                               ****************************************************99998885555555*** PP

                                 TIGR01771 207 kevrdaayeiiekKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGve 275
                                               + vr+aay+ii+ Kg T +gig ++ riv ai  de++vl++s+l ++  g+ dv+l++P+v+g+ Gv 
  lcl|FitnessBrowser__azobra:AZOBR_RS01310 211 EGVRRAAYHIIDGKGHTAFGIGGGLSRIVAAIAGDERAVLTCSILNDEVLGVPDVALSLPRVIGAGGVL 279
                                               ********************************************************************* PP

                                 TIGR01771 276 eilelkLseeEkeklkksaetlkk 299
                                               e++  +LseeE ++lk+sae+lk+
  lcl|FitnessBrowser__azobra:AZOBR_RS01310 280 ETVMPDLSEEEAAALKRSAEILKE 303
                                               **********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (313 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: 7.35
//
[ok]

This GapMind analysis is from Sep 17 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 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