Alignments for a candidate for PGA1_c12660 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for PGA1_c12660 in Azospirillum brasilense Sp245

Align D-lactate transporter, permease component 2 (characterized)
to candidate AZOBR_RS11650 AZOBR_RS11650 ABC transporter permease

Query= reanno::Phaeo:GFF1250
         (340 letters)



>FitnessBrowser__azobra:AZOBR_RS11650
          Length = 613

 Score =  167 bits (424), Expect = 5e-46
 Identities = 104/334 (31%), Positives = 173/334 (51%), Gaps = 46/334 (13%)

Query: 1   MDAILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLS 60
           M   L+Q L+GL   +   L++ GLT++FG   +VNFAHG+ +M+GA+            
Sbjct: 1   MSFYLVQFLSGLATAATLFLVSSGLTIVFGVTRIVNFAHGSFYMLGAY------------ 48

Query: 61  FETVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMER 120
                      LG  L      VE W    +G     W    A   A+ ++   G +ME 
Sbjct: 49  -----------LGWML------VERWGSTPLGF----WGAVAAASLAVGLL---GALMEV 84

Query: 121 GLIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDI 180
           GL++  Y+ P   Q+L TFG+ +V+Q+   + +G+  +       L G V++     +D 
Sbjct: 85  GLLRRLYRSPELFQLLATFGVVLVVQDAASWIWGSEDLLGRRAPGLRGSVDI-----LDQ 139

Query: 181 VYPVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGI 240
            +P++ +V      +++G ++     T +G +VRA   DR+    LG++  R FT +  +
Sbjct: 140 PFPLYDLVLIGLGPLVLGLLWLLFNRTRWGTLVRAATQDRDMASALGVDPARLFTGVLFL 199

Query: 241 AAAVAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFAS 300
            +A+AGL G +  P  + N HM M  +V +FVVVVVGGMGSL GA +A  L+G L++F  
Sbjct: 200 GSALAGLGGALQVPREAVNLHMDMAIVVEAFVVVVVGGMGSLTGAFVASLLIGQLQAFGI 259

Query: 301 MNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGR 334
           +     + P I  +++++   ++L+ RP GL+GR
Sbjct: 260 L-----VFPQITLVLVFLFMAVVLVIRPYGLLGR 288



 Score = 63.2 bits (152), Expect = 2e-14
 Identities = 76/324 (23%), Positives = 134/324 (41%), Gaps = 74/324 (22%)

Query: 19  ALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDETQKDFLGNPLKV 78
           AL+A  L L+ G  G+V+F H A F +GA+ A  +                         
Sbjct: 343 ALLAASLHLLIGLGGLVSFGHAAYFGLGAYGAALL------------------------- 377

Query: 79  KTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFYKRPHADQILVT 138
               V+ +  P          +PLA L A P++ G+G ++         +R      ++T
Sbjct: 378 ----VKHFAAP----------MPLA-LAAAPLLAGLGALVAGWFC---VRRSGLYFAMLT 419

Query: 139 FGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVW---RVVYFFFAVV 195
              A ++  V   +YG            NG++ +          P W   +  Y++  + 
Sbjct: 420 LAFAQIVWSVTFQWYGFT-------GGDNGILGVWP--------PDWAAGKAAYYWLTLA 464

Query: 196 IIGGIFSFLQ---FTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGLAGVMY 252
           + GG    L+   F  FG  +RAG         +GI++ R   + F +A + AGLAG +Y
Sbjct: 465 MAGGALLLLRRAAFAPFGYTLRAGRDSALRAESVGIDVRRHQWLSFALAGSAAGLAGGLY 524

Query: 253 TPINSPNYH--MGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFA-SMNEIKSLIP 309
                  +   M +   V + V+V++GG+ +L G V+   L  +LE+ A S  +   L+ 
Sbjct: 525 AFSKGSVFPTLMAVPVSVDALVMVLMGGIQTLSGPVVGAALFHLLETEAMSRTDWWRLVL 584

Query: 310 GIDQIIIYVVAIIILLTRPRGLMG 333
           G        + ++++L  P+G+ G
Sbjct: 585 G-------TIILVLVLAFPKGVAG 601


Lambda     K      H
   0.329    0.147    0.439 

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: 508
Number of extensions: 29
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 340
Length of database: 613
Length adjustment: 33
Effective length of query: 307
Effective length of database: 580
Effective search space:   178060
Effective search space used:   178060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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