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_RS32325 AZOBR_RS32325 PTS fructose transporter subunit IIA

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



>lcl|FitnessBrowser__azobra:AZOBR_RS32325 AZOBR_RS32325 PTS fructose
           transporter subunit IIA
          Length = 846

 Score =  455 bits (1171), Expect = e-132
 Identities = 293/672 (43%), Positives = 382/672 (56%), Gaps = 42/672 (6%)

Query: 179 GLHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEA 238
           GLHARPA  + + A+   A I +      A+AK+LVA++ L    GD++ VSA G+DA A
Sbjct: 179 GLHARPATAWVETARASAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVA 238

Query: 239 AIKALVALLAEGCGEAVVNVAEPVATQSSATLLRG------------VCASPGSAFGQV- 285
           A+  + A +         + A   A Q +   +RG            + ASPG A G V 
Sbjct: 239 ALARMKATITRLTAREKADAA--AAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVH 296

Query: 286 ------VQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQDKAA---GSAQAEIF 336
                 V V D  + + E G     E  +LTR      + L+ L D  A   G ++A IF
Sbjct: 297 VLPRAAVSVPDEPVPLIEGGDR-LHEALSLTR------QNLKALADDTARRLGPSEAAIF 349

Query: 337 RAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVG 396
            A  E+L D  L+  A +L+ EG   A++W+ A   T      L N ++A RAADL DVG
Sbjct: 350 AAQAEILNDTDLVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVG 409

Query: 397 QRVLKLILGI--QDSAWDLPER-AILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAI 453
           QRVL  I        A DLP+   ILIAE L+PS TA+LD  +V+G  T  GG TSH AI
Sbjct: 410 QRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAI 469

Query: 454 LARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAARKHQVLRHQR 513
           LAR LGLPA+    A ++ LANG   +LD   G LHL P  A+I    A    +  R   
Sbjct: 470 LARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAE 529

Query: 514 DVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEE 573
           + A+  LPA TRDGH VE+ ANV    +V  AL+ G E VGL+R+EFL+L+R  AP  +E
Sbjct: 530 EEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDE 589

Query: 574 QAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLR 633
           Q  TY  +  AL   R L+VR LD+GGDK + ++ +  E NPFLG+RG RL L RP+LL 
Sbjct: 590 QYETYRGMLTAL-EGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLE 648

Query: 634 EQFRAILASA--GFAR----LHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMI 687
            Q RA+  +A  G A+    L IM PM++ L E+   R   E     L    +P LGIM+
Sbjct: 649 TQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRAELDAPAVP-LGIMV 707

Query: 688 EVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVK 747
           EVP+AA+ ADV A HVDFFSIGTNDLTQY LA+DR HP LA +ADS HPAVLRLI  TV+
Sbjct: 708 EVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRLTVE 767

Query: 748 AAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIAR 807
            A  HG+WVGVCG +A +     +L GLGV ELS++   IP +K  +R  DL+  +  A+
Sbjct: 768 GAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQ 827

Query: 808 QVLGLEEAAEVR 819
           + L  E A  VR
Sbjct: 828 RALDCETADAVR 839


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: 1517
Number of extensions: 72
Number of successful extensions: 5
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: 846
Length adjustment: 42
Effective length of query: 796
Effective length of database: 804
Effective search space:   639984
Effective search space used:   639984
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: 56 (26.2 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:

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:

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:

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