Alignments for a candidate for Dshi_1194 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Azospirillum brasilense Sp245

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate AZOBR_RS08575 AZOBR_RS08575 C4-dicarboxylate ABC transporter

Query= uniprot:E4PQE4
         (729 letters)



>FitnessBrowser__azobra:AZOBR_RS08575
          Length = 698

 Score =  354 bits (908), Expect = e-101
 Identities = 223/675 (33%), Positives = 350/675 (51%), Gaps = 64/675 (9%)

Query: 109 AGAMLPALYVLYQTFSFWQMVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFHQRERS 168
           AG  + A+ V +  F  W    N    + V     H G+ LL       +  +  + ER 
Sbjct: 31  AGKAVFAIAVAFSLFQIWTAAFNPLSSMVVRSV--HVGFLLLMTF---TLFGFRQEAERR 85

Query: 169 VFSVPDLVLIVCSLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVA 228
                D +L + + A+  Y  V     ++ +   +   + +    IA   L+ E  RR+ 
Sbjct: 86  SVPWYDWLLGLGAFALGLYHYVFEVDLIQRAGDPNTTDLIVGALTIA---LVFEAARRIM 142

Query: 229 GMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQVYTDA-GILGPTTAVSSTYIIL 287
           G AL I+  VF+ Y   G +LP  L + G  V +    +Y    GI G  T VS+T+I L
Sbjct: 143 GWALPIMCGVFIPYALFGRHLPFGLAHRGYDVDQVIDNLYLSTEGIYGTPTFVSATFIFL 202

Query: 288 FIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSL 347
           FI+F AFL+ + +   F + +    G ++GGPAKV++ +SG MG ING+   NV++TG  
Sbjct: 203 FILFGAFLERAGMIKLFNDVSLGLVGHAKGGPAKVAVISSGFMGTINGSGVANVLTTGQF 262

Query: 348 TIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAI 407
           TIPLM + GY    AGAVEA AS GGQIMPP+MGA AFIMAE  G+P+++IAIAA IPAI
Sbjct: 263 TIPLMMRFGYRPAFAGAVEATASMGGQIMPPVMGAAAFIMAETIGVPFSDIAIAAAIPAI 322

Query: 408 LYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQC-YLFVPIIILIVALFMGYSVIRA 466
           LYF S ++MV  EA K  + G+ +D+ P +   +K+  YL +P+  L+  LF G++ + A
Sbjct: 323 LYFGSAFWMVHLEAGKHNLVGLPKDQCPSVLGALKESWYLILPLAALVYLLFSGFTPLFA 382

Query: 467 GTLA-------TVSAAVVSWLSPN------------------KMGLRH------------ 489
           G +         +   +V ++ P                   +MGLR             
Sbjct: 383 GVIGIALTVALILGTRIVGFIGPTALRVGFWVVLGLIAAALWRMGLRTEHLAFAIVGLLV 442

Query: 490 ---------------ILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDV 534
                          ++Q+L   +  A+ + V CA  GV++G+++LTG+ + F+  ++D+
Sbjct: 443 LPCLALKGGRETLALLVQSLADGAKNAVGVGVACALVGVLIGILTLTGLASSFASTIMDL 502

Query: 535 AATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVV 594
           +  + L+AL+  M   I+LG G+PTTA Y + A++ AP L+Q+G+  + +H FVFYF ++
Sbjct: 503 SGGNLLIALLLTMLACIVLGTGLPTTANYIITAAIAAPALLQMGVPLIVSHMFVFYFGIM 562

Query: 595 SAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEA-GWFEIA 653
           + +TPPVALA+ AA+ I  A  ME    + R+ +A ++VPFM  Y+ AL+++      +A
Sbjct: 563 ADLTPPVALAALAASSICRAGHMEIGWIATRVAMAGYVVPFMAVYDPALMLQTDDPLAVA 622

Query: 654 RALVTATFGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAF 713
             L  A   + +     +G+F +   +W  R+   AAA L +     TD  G  +     
Sbjct: 623 YVLFKALISIGLWGAATIGYFWT-PMNWAERVFAAAAAFLFVLSLPVTDEAGFVMTAAFL 681

Query: 714 VIQKQRKTRLATAGA 728
           + Q+ R  RL    A
Sbjct: 682 LWQRHRLRRLGRTSA 696


Lambda     K      H
   0.327    0.139    0.410 

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: 1318
Number of extensions: 81
Number of successful extensions: 5
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: 729
Length of database: 698
Length adjustment: 39
Effective length of query: 690
Effective length of database: 659
Effective search space:   454710
Effective search space used:   454710
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 (21.7 bits)
S2: 55 (25.8 bits)

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

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