Alignments for a candidate for PS417_11890 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Azospirillum brasilense Sp245

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  366 bits (940), Expect = e-105
 Identities = 206/506 (40%), Positives = 305/506 (60%), Gaps = 8/506 (1%)

Query: 21  PVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD 80
           P   P LL I  +SK F GV AL  V   VR G + AL+GENGAGKSTL+K + G+YQ D
Sbjct: 6   PTASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRD 65

Query: 81  AGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHRE 140
           AG + L G+ +       A +  I  ++QE+NL+P++S+AEN+++GR+ +  F ++D   
Sbjct: 66  AGTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMR-FGLVDRGA 124

Query: 141 MHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEV 200
           M R    +L    + LD    +G  S+A +Q+V IA+AV   + +LI+DEPT+++  +EV
Sbjct: 125 MRRRARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEV 184

Query: 201 AHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMM 260
           A LF ++  L+++G GI+++TH +++V+++ D + V R+G  +G +R   +    L++MM
Sbjct: 185 AVLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMM 244

Query: 261 VGRELSQLFPVREKPIGDLLMSVRD--LRLDGVFKGVS-----FDLHAGEILGIAGLMGS 313
           +GREL  +      P  D     R   +R  G  K  S      D+  GE++G+AGL+GS
Sbjct: 245 LGRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGS 304

Query: 314 GRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 373
           GRT  A  +FG+  +D GE  +DGQ VR+  P  AI  GF    EDRK  G+   LSV E
Sbjct: 305 GRTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRE 364

Query: 374 NMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 433
           N+ +A+         I +     + +   + L ++TP  EQ I  LSGGNQQKALLARWL
Sbjct: 365 NIILALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWL 424

Query: 434 MTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHE 493
            T PR+LILDEPTRGIDVGA AEI RLI  L ++GMA++++SSEL E++  S RV+V+ +
Sbjct: 425 ATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRD 484

Query: 494 GDLMGTLDRSEATQERVMQLASGMSV 519
              +  L   E   +R++   +  SV
Sbjct: 485 RRHVAELRGGEVAVDRIVAAIASESV 510



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 57/250 (22%), Positives = 116/250 (46%), Gaps = 17/250 (6%)

Query: 35  KGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFD 94
           +G+    ++    L +RPG V+ L G  G+G++   +++ G+ + D GE  + G+ V   
Sbjct: 275 RGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLR 334

Query: 95  TPLAALQAGIAMIHQELN---LMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQLLER 151
            P  A++ G     ++     ++  +S+ ENI +  +   G+     R + RC  + +  
Sbjct: 335 GPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWL----RPIPRCRQEEIAD 390

Query: 152 LRINL------DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205
             I L        E+ +  LS   +Q   +A+ ++ +  +LI+DEPT  I     A +  
Sbjct: 391 RFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGAHAEIIR 450

Query: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265
           +I  L A G  ++ ++ ++ E+ + +  V V RD  ++    A+   G+  +  +V    
Sbjct: 451 LIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHV----AELRGGEVAVDRIVAAIA 506

Query: 266 SQLFPVREKP 275
           S+  P   +P
Sbjct: 507 SESVPEEPRP 516


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: 658
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 521
Length of database: 516
Length adjustment: 35
Effective length of query: 486
Effective length of database: 481
Effective search space:   233766
Effective search space used:   233766
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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