Alignments for a candidate for PS417_11890 in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Desulfovibrio vulgaris Hildenborough

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  286 bits (732), Expect = 1e-81
 Identities = 177/506 (34%), Positives = 285/506 (56%), Gaps = 17/506 (3%)

Query: 8   SSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKS 67
           S+ P  G    A+  D   ++ +  + K F  V A  D+ L + PG + AL+GENGAGKS
Sbjct: 15  STTPQTGRTGRALRHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKS 74

Query: 68  TLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGR 127
           TLM I++G    D G + + G+ V F +P  AL+AGI M++Q   L+  M++AEN+ +G+
Sbjct: 75  TLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQ 134

Query: 128 EQLNGFHMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILI 187
                   +    M R  A+L  R  +++DP  +V +LS+ ERQ VEI K +  DS +LI
Sbjct: 135 SGA----WLSPVHMSRVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLI 190

Query: 188 MDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQR 247
           +DEPT+ +T  E   LF  +  +   GK I++I+HKM EV ++ADE+A+ R G  +    
Sbjct: 191 LDEPTAVLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFH 250

Query: 248 ADSMDGDS-LISMMVGRELSQLFPVREKPI--GDLLMSVRDLRLDGVFKGVSFDLHAGEI 304
              + G++ L + MVGRE+  +  V  +P+  GD ++ V  L  DG+ KG+SF++  GE+
Sbjct: 251 ESEVPGEAELANRMVGREV--ILEVAAEPLEPGDRVLHVDGLAGDGL-KGLSFEVRKGEV 307

Query: 305 LGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSG 364
             IAG+ G+G+  + E + G+     GE+ L G P R        + G A + EDR+  G
Sbjct: 308 FAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQ--G 365

Query: 365 LFPCLS--VLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGG 422
           L  CLS  +++N  +     +    F+ +K+  A   D+  +  V+    E    +LSGG
Sbjct: 366 LATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGG 425

Query: 423 NQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIY-RLISYLASEGMAVIMISSELPEV 481
           N QK ++ R     P +++ + PT+G+D+ A  E++ RL+   +  G  V+++S +L EV
Sbjct: 426 NLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEV 483

Query: 482 LGMSDRVMVMHEGDLMGTLDRSEATQ 507
           L ++DRV VM+ G  +G LDRS+  +
Sbjct: 484 LALADRVAVMYRGCFIGLLDRSDTNK 509



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 59/232 (25%), Positives = 108/232 (46%), Gaps = 18/232 (7%)

Query: 286 LRLDGVFKG---------VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLD 336
           +RL+G+ K          ++ D+  G I  + G  G+G++ +   + G    D G I +D
Sbjct: 35  VRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVD 94

Query: 337 GQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRA 396
           G+ VR   P  A++ G  ++ +   L      ++V EN    VL   +G         R 
Sbjct: 95  GEAVRFRSPKDALKAGIGMVYQHFML---VDSMTVAEN----VLLGQSGAWLSPVHMSRV 147

Query: 397 LCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAE 456
           + E   +      P+   C   LS G +Q+  + + L  + R+LILDEPT  +  G   +
Sbjct: 148 VAELAARYGLDIDPAARVC--DLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQ 205

Query: 457 IYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQE 508
           ++  +  +A  G A++ IS ++ EVL ++D + ++  G+++     SE   E
Sbjct: 206 LFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGE 257



 Score = 67.0 bits (162), Expect = 2e-15
 Identities = 55/228 (24%), Positives = 102/228 (44%), Gaps = 11/228 (4%)

Query: 43  LSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQA 102
           L  +   VR G V A+ G  G G+  L++ + G+ +P  GE+ L G P       A  Q 
Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354

Query: 103 GIAMI---HQELNLMPHMSIAENIWI-GREQLNGFHMIDHREMHRCTAQLLERLRINLDP 158
           G+A I    Q L     + + +N  +  R        +D +        +L     N+ P
Sbjct: 355 GLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEY--NVQP 412

Query: 159 ---EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGK 215
              E    +LS    Q + + +       +++ + PT  +       +++ + ++++   
Sbjct: 413 GRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA- 471

Query: 216 GIIYITHKMNEVFSIADEVAVFRDGAYIG-LQRADSMDGDSLISMMVG 262
           G++ ++  +NEV ++AD VAV   G +IG L R+D+   D++  MM G
Sbjct: 472 GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAG 519


Lambda     K      H
   0.321    0.137    0.391 

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: 624
Number of extensions: 38
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 521
Length of database: 524
Length adjustment: 35
Effective length of query: 486
Effective length of database: 489
Effective search space:   237654
Effective search space used:   237654
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: 52 (24.6 bits)

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