GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Erythrobacter gangjinensis K7-2

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_047006477.1 AAW01_RS01960 ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_001010925.1:WP_047006477.1
          Length = 315

 Score = 99.8 bits (247), Expect = 1e-25
 Identities = 73/221 (33%), Positives = 117/221 (52%), Gaps = 12/221 (5%)

Query: 1   MANTILEMRNITKTFPG-VKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSG-VYPAG 58
           M + IL++R++ KT+ G VKAL  V+L ++ GEI AL+G NGAGK+TL+  + G V P G
Sbjct: 1   MTDPILDIRDLEKTYDGGVKALGGVDLTIRAGEIFALLGPNGAGKTTLIGAVCGMVRPTG 60

Query: 59  TYEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQ 118
              G I   G           +DIG++   QEL+     ++   +       S G+    
Sbjct: 61  ---GTIRAFGMDMATHWKAARKDIGLV--PQELSFDMFDTVIRQVRF-----SRGMFGCP 110

Query: 119 QTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178
                  ++LK + L +  ++ I ++  G ++ V IAKALS   KLL LDEPTA ++   
Sbjct: 111 PDEAVIEDILKSLSLWDKRDSQIRELSGGMKRRVMIAKALSHDPKLLFLDEPTAGVDVEL 170

Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDG 219
              +   +   R +G+T I+ TH + E  ++AD++ V+  G
Sbjct: 171 RRDMWRQIDALRTRGVTIILTTHYIEEAEEMADRVGVISKG 211



 Score = 67.4 bits (163), Expect = 7e-16
 Identities = 56/213 (26%), Positives = 107/213 (50%), Gaps = 21/213 (9%)

Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337
           + L  +++T+R GE+  + G  GAG+T    +V G     R TG   I    +D++T  K
Sbjct: 20  KALGGVDLTIRAGEIFALLGPNGAGKTTLIGAVCGMV---RPTGGT-IRAFGMDMATHWK 75

Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLAN-LAGV--SKASIIDDIKEMKVASDFRTR 394
           A    +  V ++   L   + D ++     +  + G    +A I D +K + +     ++
Sbjct: 76  AARKDIGLVPQE---LSFDMFDTVIRQVRFSRGMFGCPPDEAVIEDILKSLSLWDKRDSQ 132

Query: 395 LRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQL 454
           +R            LSGG +++V+++K L  +P +L LDEPT G+DV  + +++  I+ L
Sbjct: 133 IR-----------ELSGGMKRRVMIAKALSHDPKLLFLDEPTAGVDVELRRDMWRQIDAL 181

Query: 455 AADGKGVLMISSEMPELLGNCDRIYVMNEGRIV 487
              G  +++ +  + E     DR+ V+++GRI+
Sbjct: 182 RTRGVTIILTTHYIEEAEEMADRVGVISKGRIL 214


Lambda     K      H
   0.316    0.135    0.374 

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: 359
Number of extensions: 21
Number of successful extensions: 4
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: 512
Length of database: 315
Length adjustment: 31
Effective length of query: 481
Effective length of database: 284
Effective search space:   136604
Effective search space used:   136604
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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:

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