Aligments for a candidate for treEIIA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for treEIIA in Azospirillum brasilense Sp245

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate AZOBR_RS18900 AZOBR_RS18900 peptidase

Query= reanno::WCS417:GFF4500
         (838 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS18900 AZOBR_RS18900 peptidase
          Length = 766

 Score =  251 bits (641), Expect = 1e-70
 Identities = 192/612 (31%), Positives = 299/612 (48%), Gaps = 32/612 (5%)

Query: 234 EDAEAAIKALVALLAEGCGEAVVNVAEPVATQSSATL---LRGVCASPGSAFGQVVQVTD 290
           E  +     +  L+A+G    +VN  E  +T   A L   L G   + G A G  V +  
Sbjct: 159 ETLQTIAMVVAELVAQG---ELVNPQEVASTGDPALLPARLSGTSLASGLAMGLAV-IHR 214

Query: 291 PELVITEQGTGGA-TERAALTRGLLAANEALQVLQDKAAGSAQAE---IFRAHQELLEDP 346
           P+L I +  +  A +E A L   +   + A+  L + AA +  +E   I   ++   ED 
Sbjct: 215 PQLTIRQMVSEDAESELARLNAAIATMHSAIDDLLNAAALAGLSEPKDILETYRMFAEDR 274

Query: 347 TLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGI 406
             L      +  G +A  A       T      L +  I ER  DL D+  R+L+ + G 
Sbjct: 275 GWLSRIREAIRMGLTAEGAVQQVQNDTRARMSHLTDPYIRERLLDLEDLTNRLLQHLAGR 334

Query: 407 QDSA--WDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAIC 464
           +  A    LPE  +L+A  + P++    D R++ G +   G  +SHV I+ARAL +P + 
Sbjct: 335 KSEADGGTLPEDIVLVARSMGPAELLDYDQRRLRGVILEEGSPSSHVCIVARALNIPVV- 393

Query: 465 GVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQA--SLPA 522
             P  +  +     V++D D G+  + P  AE  Q+  A    +   +  + +A  + P+
Sbjct: 394 QAPDALNRIEPLDPVIVDGDHGQAFVRP--AEDIQMAFAEAVALRARKEQMYEAIRAQPS 451

Query: 523 TTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIA 582
            TRDG  + +  N   L ++ H    G EG+GL R+E  ++ R+  P    Q   Y+ I 
Sbjct: 452 VTRDGVPISIQLNCGLLIDLPHLKASGAEGIGLYRTEIPFMVRSTYPDVHAQTDLYSRIL 511

Query: 583 RALGTERNLVVRTLDVGGDKPLAYVPM-DAETNPFLGLRGIRLCLERPQLLREQFRAILA 641
                ++ +V RTLDVGGDK L Y+   + E NP LG R IR+ L+ P LLR+Q RA+L 
Sbjct: 512 DQTD-DKPVVFRTLDVGGDKMLPYIAASEGEENPALGWRAIRIGLDHPSLLRQQLRALLR 570

Query: 642 SAGFARLHIMLPMVSLLSELHLARKILEEEALAL-GLTELP----KLGIMIEVPSAALMA 696
           ++    L +M PM++ ++E   AR++L+ E   L G    P    ++G MIEVP+     
Sbjct: 571 ASAGRPLSVMFPMIAEVAEFDAARRLLDLEINRLKGQGGEPPSRVRVGTMIEVPALLWQL 630

Query: 697 DVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWV 756
               P VDF S+G+NDLTQY  A DR +PR + + D   PA++ L+   V+A    G  V
Sbjct: 631 PALLPRVDFLSVGSNDLTQYIFASDRGNPRTSGRYDPLSPAMMSLLRRLVEACGDAGVPV 690

Query: 757 GVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLG---LE 813
            +CG +A   L    LIG+G   LS+S P +  +K  +R LD+A    + RQ +    L 
Sbjct: 691 SICGEMAGRPLDAMALIGIGFRTLSMSPPSVGPVKTMLRSLDVA----VLRQYMNGLYLR 746

Query: 814 EAAEVREALRQY 825
               +R+ LR +
Sbjct: 747 GDHSLRDKLRSF 758


Lambda     K      H
   0.318    0.133    0.371 

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: 1343
Number of extensions: 64
Number of successful extensions: 6
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: 838
Length of database: 766
Length adjustment: 41
Effective length of query: 797
Effective length of database: 725
Effective search space:   577825
Effective search space used:   577825
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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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Protein sequences (fasta format)
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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, or view the source code.

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